three possibilities that I can think of directly:
1) you're storing the project in a cloudsync'ed folder (in the case of Microsoft OneDrive that might even be without your knowledge).
The RMs access their files like a database (constantly open) instead of only when saving, because the amount of data is too high to use regular file operations. And that means that any cloudsync whith the editor working has a chance of destroying those files.
Please store the project outside could-folders and only use clouds for distribution and manual backup.
2) your antivirus gets a false positive on RM because RMMV and RMMZ use HTNL5-Technologies with local file access.
Most Antivirus and similar protection programs can't detect the difference between a local HTML-file accessing local files and a remote website trying to infect your computer.
Add RMMV/RMMZ to the whitelist of all your protection programs (not only antivirus, there might be others)
3) your harddrive is near End-of-Life and has to remap failing storage sectors. This usually takes a ten-year-old harddrive under regular working conditions, but a bad ventilation or other overheating causes can age a computer much faster, resulting in similar effects after one or two years of service in a hot environment.
save your project externally and purchase a new harddrive to replace the current one if a program like checkdrive reports a S.M.A.R.T.-status of below 50% (normal is 80% or above, a number <50% means you're only a few weeks or months away from total failure)