I only have one Preference stored: Do not edit in Lower Zone.
Input and Output routing is stored per project so no problems there, and most other data is as well with the exception of timeline settings and quantization (hint SB).
I delete my prefs any time I have an issue or crash, update and clean Windows; I’ve only once had a problem with project corruption and it was going from a really early version so keep archives of any changes no matter how small (or big) the file or change to the data is.