Audio Chunk Shifted in Time, Nonsynchronous Waveform, Vanishing FX (Solved)

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.

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.

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.

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.

bitSync
 
Still don't know what happened with the pans, levels and FX but that was easily fixed.
 

 
Any chance you pressed "O" for Offset mode?