@Nianoniaa I doubt the files' content is getting zapped by a "legitimate" write to the file, more that something nasty is causing the underlying disk area to get corrupted. In itself I can't see that Qt would be the cause. However you probably do a lot more reading/writing of files etc. when you compiling or clanging than in other situations, so the problem may be more likely to show up then.

Hi @BenjaminHabegger, AFAIK, the pro.shared was never not thought to share build-related settings, as that would require to have the same Kits on each installation. It may work nevertheless. Have you read the sentence "Note: You must always specify the ProjectExplorer.Project.Updater.FileVersion variable and use the same value for it as in the .pro.user file." from your shared doc page? Have you compared the FileVersion with your pro.user file? However, to solve your original problem, you can vote for QTCREATORBUG-18414.