I'd like to recount each step for you but I don't think I can comprehensively.  This is as close as I can get...
 
I was working on a song I recorded, just acoustic guitars and vocal, no click, 7 tracks total.  I was fixing to do some other things where I felt a tempo map might be useful.  In preparation for that I recorded a MIDI Instrument track and got a MIDI event track synchronized with each beat of what I had recorded earlier. Upon finishing the recording I went back and tweaked the MIDI timing in the PRV until I was satisfied.  So far so good.  Never got to the tempo map.  I left the PRV and went to audition the progress so far.  Before doing so I added a couple of busses and did some rerouting.  Then, when I went to audition I discovered the names of the FX I had in the tracks and the master buss were greyed out (but the baby blue power lights were on) and were inaudible: Breverb, VX-64 Vocal Strip, iZotope RX3.  I saved and closed the project then reopened it.  The FX were back in baby blue and now audible but I had a bizarre new twist.
 
Before closing the project, the guitars, vocal and MIDI were in all sync.  Upon reopening and playback the MIDI and the guitars were in sync, and the vocal started in sync up through about the first 35 seconds, but the verse now starts (0:53) about 3 seconds before it should (0:56) and about 3 seconds before where the waveform shows it should.  At 1:15 the end of the first verse is truncated by a replay of the last 3 seconds on the first verse, thus getting the remainder of the song back in sync.  It's as though the part of the vocal after about 0:35 or so got moved backward/earlier 3 seconds and at 1:15 whatever happened stopped happening and the original recording reappeared; from this point onward everything's cool.  And especially weirdly, the waveform shows the vocal starting at 0:56 where it should, which is to say you can hear the vocal about 3 seconds before the waveform shows it's there.  There are no splits in the vocal track.  I shut X3 down and reopened and the vocal track audio and waveform disparity persists.
 
What do you think?  Should I just 'save as' or export individual tracks and try to fix it in a new file?  Ever seen this kind of weirdness?  Thanks.
 
 
P.S. - Also, I should mention that when I added the two busses, the moment I routed the 6 guitar tracks to them the pans went to center and the levels went to 0db, so I lost the panning and the levels.
 
 
P.P.S. - The nonsynchronous weirdness between the audio and the waveform as well as the redundant 3 seconds on the end of the first verse appears to apply to all takes in all take lanes of the vocal, although I only checked the most recent several takes.

The greyed out effects sound like the effects were disabled probably by the keyboard shortcut "E". The FX button would be green in the Mix module. This would affect PDC. That said, it would not explain the time shifts being observed so more than disabling effects occurred. I doubt "Save As" would fix any problems because all it will do is copy the project as is, aithough it be a simple fix if it works and easy to test.

scook
The greyed out effects sound like the effects were disabled probably by the keyboard shortcut "E". The FX button would be green in the Mix module. This would affect PDC.

I could have fat-fingered the E key for sure, and thanks for the knowledge nugget; never used that shortcut before.  Didn't notice any greenness in the Mix module, which doesn't necessarily mean there was no greenness, there could have been I suppose.  This would explain the center pans and the 0db faders, right?
 

scook
That said, it would not explain the time shifts being observed so more than disabling effects occurred. I doubt "Save As" would fix any problems because all it will do is copy the project as is, aithough it be a simple fix if it works and easy to test.

 
I wasn't thinking Save As would fix things but rather it might give me a more stable project base to continue to work with.  I don't recall how many undo levels I'm set for, but I'm thinking of Save As to yank out the MIDI track, then undoing, if I can, back to before all the badness happened.  I should have done a Save As the moment things blew up and I could have attempted the undos on the original project while protecting other progress I had made.
 
I just don't know if I'm going to be able to fix the 18 takes that are all identically mangled (the audio chunk slip/overwrite that is misaligned with the waveform).  Those takes had a comp in their future but that just might not happen.  I may have to re-record the vocal.
 
Scook, always appreciative of your feedback.  Thanks.

There's another important piece to this I neglected to mention.  In preparing to add the MIDI guide track for tempo mapping I computed the amount of time it would take to have the downbeat of the start of the song on beat 9.  As it was, the song started on a vocal count-in without regard to any timing from 00:00:00.000.  I measured the first several beat intervals of the song and took their average (00:00:01.419 or roughly 70.5 BPM) to use in computing where bar 1 of the track should start.  I had enough lead in for maybe 6 or so full beats only, so I had to shift the entire recorded contents of the project right in time roughly 3 seconds.  This way I had the correct amount of time to get 8 equally spaced/timed beats in front of the downbeat on measure 9.  The timing seemed to work out perfectly as there's a short vocal improvisation before the first verse that lined up where it should and the downbeat of the guitars start lined up perfectly on 9.  It's just that a little later in the track is where the vocal precedes where it should by about 3 seconds.  It seems the 3 seconds track shift is too close to the audio/waveform mismatch to be coincidental; I'll measure it later to see if the time disparity on the vocal track is identical to the mismatch in the audio and waveform.  But if the problem in the take lanes is associated with the time shift performed equally and concurrently on all recorded tracks (Select All, then Move), it still doesn't explain why only an identical segment of all of the take lanes has this bizarre audio/waveform mismatch and why the entire track isn't affected.
 
The end effect is though all but 3 seconds of the first verse was copied onto itself (overwritten) in the exact position it was in in time prior to sliding the tracks to the right 3 seconds, like a part of the vocal track plays back from where it used to be before the track (and its waveforms) were slid to the right 3 seconds.  So the verse vocal, at some distance into the track, now starts about 3 seconds early, perhaps where it originally did before the track move, and when the weirdness stops, the vocal as moved 3 seconds to the right/later is aligned with the rest of the music and with the waveform.  Of perhaps 4 take lanes auditioned, this weirdness is identical on all of them.
 

Wait, there's more!
 
I think I may have figured it out.  I completely forgot that I had Melodyne in the FX bin of the voice track and that I had transferred the first verse into Melodyne for some tweaking.  I did the Sonar track shift right/later *after* transferring the verse into Melodyne.  I believe Melodyne is playing back the first verse where it was originally located in time, 3 seconds earlier than the now-shifted-audio in Sonar, and when Melodyne is done its segment playback it allows Sonar to playback the last 3 seconds of the originally recorded, now-shifted-later voice track.  The waveform for what Sonar is aware of is correct.  The Sonar waveform just doesn't reflect what Melodyne is playing back (to the exclusion of the track audio in Sonar) at the point where it originally ingested the voice track segment.  I'm nowhere near my DAW at the moment but I'll test this theory when I get back to the studio.
 
See, the problem with all this crazy DAW recording business is you need to be as smart as your software.  So I guess I'm doomed.
 
As far as recovering from my ignorance goes, I think I've configured my project saves to do new files with each save, so I should be able to dig deep enough to unearth a recoverable version.  I may be OK...   ...this time.

Yep, I malevolently Melodyned myself. Did a transfer of the first verse into Melodyne, then later shifted the track audio in Sonar to be later.  Melodyne plays back at the original temporal position of the transfer, of course.  If I turn off Melodyne on the vocal track my problem goes away.  I even read about this in the Melodyne manual. Now I feel as though I've learned through some life experience.  We'll see about that.
 
Still don't know what happened with the pans, levels and FX but that was easily fixed.
 
Cheers all.

Have you tried using Melodyne as a Region FX instead of in the FX bin?

Read about it, not tried it yet.  I understand there are a number of benefits from the DNA ARA integration using it that way.  I'll try it over the weekend.  Thanks again, Steve.

Using Melodyne as a Region FX has nothing to do with Melodyne features like DNA. It is all about where Melodyne operates in the signal flow (illustration from http://www.cakewalk.com/Documentation?product=SONAR%20X3&language=3&help=Mixing.07.html). Notice where Region FX happen in the signal flow diagram, they work at the clip level before track processing like the FX bin.

Yeah, I meant ARA.  Thanks.