Server.ini for dedicated servers overwritten to a blank file

Hello, I have noticed on a few of my servers (over the course of this weekend, since the Friday update) that several of my server.ini's (upon server launch) were overwritten to empty files, which means that they defaulted to the default port (10999) and therefore failed to launch, since that port is already in use by another server. I have observed this issue in the past after updating game files, and am curious to know if there is a fix to this. It is deeply annoying to deal with, an absolute pain in the neck because I host a large number of dedicated servers and having ports changed around like that disrupt my ability to host substantially. 

NOTE: rerunning the installation appears to have fixed this issue. Bizarre that it is an issue in the first place though. 

Post edit note: I notice on server launch (my platform is Windows Server 2019) that the server.ini is by default modified upon server launch, as indicated by the time stamp. cluster.ini is not altered in any way whatsoever though, only read from. Is it necessary to have the game modify server.ini on each launch? Almost all server hosters/even regular players would have no need to modify server.ini on a regular basis, so I am genuinely curious why this is a thing. (NOTE: I add two auxiliary folders to my server save folders, one for keeping a master template of worldgenoverride.lua (I do not like how the game overwrites these; I prefer keeping a formatted and commented master version of the file in case I need to change any world settings in post) and one for keeping crashlogs for reports like this.