I've been playing the server for about two weeks now, and last night when I tried to start Royals up I got a prompt telling me that the shortcut was no longer useable since some files were moved/deleted. I tried reinstalling and windows detected malware after installation and removed it before I could look for a solution. I've tried this several times now and it keeps removing the files before I can get to them. What can I do to prevent this? I'd rather not turn off all the antivirus measures on my pc though.
You don't have to completely turn off your anti-virus. Just add the MapleRoyals folder to your whitelist.
What kind of virus protection do you use? Like what Ponder said, you need to add the MapleRoyals.exe under your White List/Exception List through your anti-virus, so it will not delete your file.
You might need to make an exception for the whole directory so this one should be excluded "C:\Program Files (x86)\MapleRoyals\"