Install not completing properly, files not getting deleted etc.?

Took a copy of EFT folder straight after performing upgrade to 0.12.10.12192 via BSG launcher. Downloaded SPT-AKI 1.3.0, extracted into the copied EFT folder, as per previous installs. Ran Server.exe noticed that files e.g. Battleeye did not get deleted, also I did not see the usual cert generation messages in the server window, but yet I do have two cert files in the expected folder.

SPT launcher opens fine, create new account etc., but I am worried that install did not complete properly as files I saw deleted in previous SPT installs (as recent as 1.2.0) as still there.

I even tried running Server.exe as Administrator, hoping to see the black terminal/batch window appear to do the deletions, but no difference.

Any ideas please?

Here is the contents of my folder, after running Server.exe

Yes Zew I started the launcher after the server was running, created a new account etc.

I have not yet clicked the "Start Game" in the launcher, because I am worried about BE etc. being triggered, as the file is still there.

IIRC on the last number of installs I have done the files got cleaned up as part of running Server.exe for the first time, but I may be misremembering things!

Thanks Zew all seems good after running the game. Guess I was spooked by not seeing the (blue?/green?) text at the top of the server window when it was run for the first time, post-install, regarding generating the certs. Maybe I just missed it, or maybe the devs removed those messages?