I just noticed this morning that the same thing is happening to me. Files that were added while Insync was offline are deleted. It's as if it syncs from Google first, so since those new files didn't sync and aren't in my Google Drive yet, they just get wiped out as if I had deleted them from Google instead of being uploaded. This is very not cool, as I'm now deeply concerned about what I may have lost without even realizing it. I guess I'll go dumpster diving in the Google Drive Trash and Insync trash now.
Also wanted to note, at least some of the files that were deleted are NOT in the Insync trash, so there's no real way to know what's been lost. Thankfully, this has happened before, so I back up my Google Drive folders with Crashplan too.
Let me know where to upload my logs, maybe that will help. Thanks!