Files disappearing, or being wiped in the past few weeks
This thread is stale. Please consider creating a new thread before replying to this one.
uMod Admin
Sorry for the delay in replying, were you able to figure out the cause?
Original Poster
Funny, I been just dealing with it and I found it to happen when you either shutdown the shutdown process early, or when a bad parameter in launch causes an error. 
I literally watch the files dissappear in these cases when I reproduce the condition and the explorer window is open. It's always after the error, then poof, the files dissappear before my eyes. 

Then when I was going to respond to your mmessage, I thought "what if I check my AVG quarantine?"
OMG, YUP! There is RustDedicated in there 5 times.
AVG is the culprate! 

They are detecting RustDedicated.exe as IDP.Generic.

I dont see my launch script in there at all but AVG is deleteing that as well. Probably because it knows RustDedicated.exe is in the rust.bat window, so it deletes both.
And I run AVG in silent mode because I dont want it harassing me for everything I want it to do, so is was doing it silently.
So I assume "IDPgeneric" is a false positive? It only detects it when unity is using it, but if I right click and scan it with avg, nothing is detected. 

This is the second time AVG is the issue in the last few weeks.
They were intercepting my DKIM signed emails from my mail server, changing the header and causing me to fail DKIM. And I never use email scanning function. I moved the email server to a machine that had it installed.
That was when I was jugling servers and machines around to host the web and database on Linux, because windows 7 is about done.

Edit: There are threads about this under steam, stack exchange, and everywhere , usually pointing at Avast behavior shield for files behaving like malware. I just reconfigured AVG turning off their behavior shield. (i dont have Avast), but AVG has the same thing, and had detected the oxide compiler once before.
The new unity definantly does something that causes behavior shield to be triggered, lol.