Here is a fixed version of that file "neg_07Oct.sky". You can your copy of that file and then you will be able to open it in Skyline. Skyline will warn you that the file has been changed and does not match what the Audit Log says it should be, but you can safely ignore that warning.

It seems that Skyline has a bug in it, and the Transition List that you inserted resulted in a document which cannot be reopened. This has something to do with Skyline assigning the wrong mass to the heavy precursor transitions.

It was very helpful that your audit log contained the text of the transition list that you pasted. This enabled me to reproduce the bug that you ran into.
After you inserted your transition list, you ended up with a lot of things that looked like the attached image "InvalidHeavyPrecursorTransition.PNG". There is a heavy precursor there "336.1296" but the precursor transition thinks its m/z is "330.1095", which is invalid. As a result, you will be unable to open this document after you save it.

I will try to find someone to fix this bug.
-- Nick

Uh oh. It happened again. I recall you included instructions that allowed me to fix the files (although at the cost of opening the file repeatedly and then again as a text file to fix the errors line by line). I can to do it again, but before I do, has anyone found a workaround or a fix yet? The most recent update doesn't appear to handle it either.

I believe we managed to fix this bug back in November:
https://skyline.ms/issues/home/issues/details.view?issueId=841

So, if you are using Skyline version 21.2 which was released last week, it should not be possible for you to hit the same error that you were hitting before.

It is possible that we did not actually fix this bug, or it is possible that you are running into a slightly different bug. If you upload your files to https://skyline.ms/files.url again I will take a look.
-- Nick

I actually last saved the file before I updated, so I will go through and fix the broken ones and hope it doesn't happen again. If this helps at all, one thing I noted is that (I think) this error only occurs if I leave Skyline open for a while on my desktop (as in multiple days). Knowing nothing about how these things interact, maybe something happens if I put the computer to sleep during this period.

If it's not too much trouble, could you send us your .sky file and the .skyl file (if you have one)?

The .sky file will tell us exactly what is wrong with your file, and, also, the first line of the file will tell us which version of Skyline you were using when you saved it.
The first version of Skyline-Daily which had this fix in it was 21.1.1.316, so, if the version that created this file was greater than that, then we definitely either did not fix this bug properly, or there is an additional bug that we need to fix.
The .skyl file will contain a record of exactly what you pasted into the Insert Transition List dialog, etc.

I am not sure the exact details of what was required to hit this bug, but it had something to do with inserting a transition list that has both light and heavy transitions. If you are using an older version of Skyline without this fix, your document is doomed as soon as that transition list gets inserted. Skyline has an inconsistent idea as to what the masses of the light and heavy precursors are, and when you save that document, there is no version of Skyline which will be able to successfully open that .sky file.
-- Nick