I just had this happen last week, similar to @JimWoodhead (running both 4.30 and 4.40 MAS 200 on the server.
I had gone into Company Maint to start the test upg Data Conversion but got a message that said there's data issues that must be fixed first. Well I had already done that during the pre-Migration - so I decided I'll try re-running the migration. But first let me delete the apparent bad company data. Oooof. It started to delete the Live data folders although it couldn't finish completely because users were in 4.30 - but the damage was done. Luckily I had the manual bkup I had first made earlier.
Thought it may have had something to do with both Appl Servers running, so decided to run 4.40 MAS 200 ""as MAS 90"" (i.e., pvxwin.exe: run ""startup.m4p""). Definitely gonna keep my eye on it. Seems like this is isolated to MAS 200?