I am working on mixing a feature film that was given to me basically as-is (one hour 33 minutes, with 14 tracks dialog and sound effects in no particular arrangement).
I am mixing it and also adding more sound effects, ADR, dialog, etc.
I mixed the first 5 minutes of action sequence which requires a lot of panning, volume changes, etc then moved to the next few scenes which are primarily dialog then got to the next action sequence.
I then went back to check that the first 25 minutes flowed and found that much of my automation has disappeared: what used to be a close-to-but-not-quite peaking sequence is now going over by several dB. I have no disabled any FX, but do see that what used to be solid volume automation are now dashed.
I know X3 Producer isn't supposed to have limits on such things, but has anyone found that too many automation nodes wreaks havoc? The director is supposed to come by this evening and discuss progress, and I now have to figure something out.
 
 
 

Upon further working with the project, it appears it may be an issue with linked clips and not necessarily one of automation.

I can't comment on linked clips, but I've never had any problems with having absolutely loads of automation operating within complex projects.

Same here - I've never come across this myself. 
 
If you had linked clips, it's possible that deleting clips also removed others.  And if the setting to "Move automation with clips" was enabled, which I think is by default, I'm not entirely sure what would happen when those clips were deleted.    FWIW, the dotted display often indicates an envelope line without nodes; e.g., take an existing envelope and delete the nodes at both ends.
 

It's a stumper. : my thinking is the project became corrupt, as the missing automations have no relation to placement or relative time when when they were created (e.g. something was happening to the History for whatever reason). A few tracks completely lost all the nodes, while others only lost bits; some linked clips changed from their original link to ones that were incorrect (I was layering sounds and one track's links became the same as an adjacent track's, plus, weirdly, a time shift). I was getting the occasional white screen which would last longer than I cared or had time for, so I'd close SONAR and then either restart or logoff/ login as SONAR- in most of the white screen incidents- wouldn't release from memory; I also received the message that some hanging was caused by Izotope's Insight, so that's going to be used sparingly, now, and removed when not in use...just in case.
 
Regardless: I did a "Save As..." and copied all the relevant data to a new project, which consolidated the data in the Audio folder and things seem to be much better. I also started using automatic versioning which has saved some grief; I habitually save every few minutes or after so many steps, having been weaned on Windows 3.1/ 95/ 98/etc, but having an automatic BU version is very very nice when things get wonky.
 
And that's my tale so far. 
In case you're curious, the movie I'm working on is "Now Hiring", which when all is finished will have been mixed completely in SONAR X3 Producer.   
 
Cheers!