I have a similar issue in my current save with a created nation. I submitted the issue in the bugs section earlier tonight and will see if we get a response.
I am the most successful club in the nation and before competing in Europe for the first time a few seasons ago my club reputation was in the 2100-2200 range. Now during my first season in the Champions League group stages with 7 points with wins against Juventus and Feyenoord, and a draw was AZ, 3 seasons of making the Europa League Round of 16 and a Conference League play off round, the reputation has dropped to 691.
My league has been climbing in the competition rankings dur to my success, yet my club reputation is in the toilet, does make me think that there is a bug where smaller nations clubs are having the reputation points for success in Europe someone being applied as negative rather as positive. It maybe all clubs, but my small ranked nation, along with your San Marino save are noticing the reputation decreases a lot more.
I have been using this file for years on FM, with tweaks every game, but this is the first time where this has happened.
Edit: Should have included the top clubs as well, so show that they are national rep, where I once was.