I think this is a bug in the windows deployment, we've encountered the same problem. We found out after the service had some troubles starting up, took over 30 minutes sometimes.
fill in a support ticket to Mendix.
Hi, In our case the temp files turned out to be generated by a custom java process. The files should not have been created (and as such we corrected the code). Issue solved. I checked with Mendix and they indicate that files in the mentioned temp directory are always allowed to be deleted (except for the very recent ones since they might be in use at that moment). Kind regards, Brian