Not to resurrect a dead thread but I found a trick that helped me and want to pass it on to anyone who has the same problem (and poor source control)
As Stubon mentioned, trying to copy and paste the block diagram contents to another VI left big gaps in mine as well. It basically was the largest structure containing the offending code (in my case a sequence frame but I am guessing this may be similar for any structure), so I copied its contents and pasted. Again some of the code copied but there was a for loop that did not. coping its contents to a new VI revealed a single item that did not copy. In my case an express elapsed time VI. This failure has happened to me twice where the culprits were two different express VIs and WVisser also mentioned an express VI causing the issue for him. Seems to be a common thread.
anyway the basic steps to hunt for the error (for me anyway) are
1) select all in the block diagram and copy
2) paste into a blank vi.
3) look for holes (a missing structure of some kind or a single VI). Once identified you can close this new temporary vi without saving.
4) on the original vi, select the contents of the structure that didn't copy (if it is a structure with multiple cases/frames/etc. you will need to do each cases contents individually) and copy them
5) iteratively repeat steps 2-4 until you find a single item that doesn't copy.
6) replace the offending item on the original broken VI and then you should be able to save.
If you use this method and find the offender, maybe reply to this thread with what the offender was. Maybe this can help NI can fix the issue.
