Hi, just circling back to this issue. Sorry for the delay.
I'm a little unclear on why things don't work for you if you simply move the .indigostack file out of
~/Documents/Indigo to somewhere that iCloud will leave it alone. I am not aware of any reason you'd need a symlink or anything. Indigo saves new stack files to your Documents folder but any time after that you can move that file anywhere you like and Indigo should use its new location from then on.
Besides the above, I'm curious how your Mac is configured so that it does this auto-deleting thing. I assume it happens if you have both...
System Settings > Apple ID > iCloud > Optimise Mac Storage turned on
System Settings > General > Storage > Store in iCloud > Desktop and Documents turned on.
I can't really replicate the problem because my (free plan) iCloud is way too small to hold what's in my Desktop and Documents, and Apple in their infinite wisdom block you from using iCloud in VMs.
From a technical perspective I think the correct fix is for FSEvents to disambiguate between a file deletion and a file-deleted-by-iCloud-but-still-kinda-there situation. However I'm not turning up a lot on this front. Will keep digging.