windows 10 22h2
shoutcut 24.04.28
to recreate. split a video sample several times, so that there are many sections. create filter-mask-draw(glaxnimate), and new - creates a new glaxnimate rawr file starting at 1.rawr .do this 4 times on different split sections so you have 4 glaximate files numbered 1-4.
now split the first video section to which the filter file 1.rawr is applied. To the second part, select the mask-draw(glaxnimate) filter, and click on new. glaxnimate will open with a new 2.rawr file, and the original 2.rawr and also 3.rawr and 4.rawr will have been deleted from the project directory.
Obviously when you have tens of filter files this is somewhat catastrophic, as they were removed from your hard drive/ssd
fortunately a copy can be found in c:\Users*username*\AppData\Local\Meltytech\Shotcut\autosave (thank goodness!) but they should not be auto-deleted from the project directory, and the “new” function for mask:draw (glaximate) should be safer
eg, if nextnumfile exists increment count and check again.
That is very strange behavior. There is no code to remove those files when clicking New, and autosave is not intended to backup .rawr files–only .mlt project files. This makes me think that you somehow ended up editing a project file that is in autosave. A “project folder” is simply a flag in the project file that says to use the document’s folder. Then, when using New with a project folder, it tries to create new files in there using a simple code like:
With a counter X starting at 1, if project/X.rawr does not exist then use that.
Did you ever get a dialog asking to recover an auto-saved file and choose yes, or did you manually open a project from the autosave folder?
I did find a bug that when Shotcut UI offers to recover an auto-saved file, it incorrectly uses the autosave folder as the project folder instead of the original file’s folder. I suspect this happened to you. The problem only exists during the app session immediately upon recovery. If you reload the project from its original location thereafter, it should not. Possibly, you added the Mask:Draw filter (or clicked its New button after Split) a few times during the recovery session, which automatically generated them in the autosave folder (wrong).
Strangely in the project I am working on there were 3 rawr files in the project folder and all the others (27 of them) had been moved to the autosave folder. I’m not sure why they were all moved there, as I’ve never edited more than one glaxnimate rawr file at a time.
The problem appeared to occur when clicking new when an existing rawr file was already selected for the filter.
I did have some times when glaxnimate crashed (closed itself) when I accidentally left and right-clicked the mouse at the same time while editting. (if that helps) 
You did not answer my question. Shotcut does not move files to the autosave folder; it only copies a .mlt project file to there. The only way they could get there (not including user manual file management) is by one of the recovery methods I mentioned above: Shotcut offering it to you, or you opening it directly. Users are not supposed to directly open projects from the autosave folder. And once you do, it gets added into the Recent list and you might choose it again. I fixed the bug with the wrong project folder used during the app session immediately after recovery. I was not able to reproduce the bug following your steps.
clicking new when an existing rawr file was already selected for the filter
That does (and should) create a new file regardless.
sorry, I don’t recall if shotcut crashed and popped up with an “autosave recover” message, but when the glaxnimate files disappeared, I did close it (shotcut) and reopen it, selecting the project from the actual project location, not the autosave folder. The reason I noticed the rawr files were not there was because it was opening the project folder, and the other files were no longer there. I was not aware of the autosave location until I checked my project file, and a number (but not all) of the rawr files were in the autosave location.
so, to be clear, the project file is in the project directory, but most of the rawr files were moved? into the autosave directory. I’m sorry I can’t recall more useful info at the moment.
I will say that shotcut itself is much more stable than earlier versions, which is great.