Alright, so I've heard of this same issue elsewhere in another thread which in-game commands will not seem to save the change. There was no solution, however, there are several things you may still do...
You could try saving the server right after making the in-game change and see if that resolves it, although could be quite annoying especially on larger servers.
Check the command code itself and see if you can spot the issue. (If you can locate that code anyway)
Come up with some type of work around such as executing a function in a script that sets the new skill cap of an X amount.
I was studing the CharacterCreation Script just this morning and figured out how to set a new statcap, skillscap, str, dex, int, starting location and more. Although previous coding experience greatly helps. But my point is that it does change skills and skillcaps which can teach you how to do that stuff specifically. (If needed even)
