I know that Additional CP reset on save/load, but it can be built up very quickly(if you distribute your skill points properly), so I decided the game doesn't keep them.
The second issue may need to be checked. Thank you for reporting!
I tested it again. As you said, if I dump some points to Increased and More upgrades after level 100, the game seems to enter a positive loop state. Hits 3000 level so easily.
This is not a problem under the 100 level, but I may fix the highest XP reward if I get more feedback.