Is upgrading a nightly build supposed to clear out options?

I've noticed a few times that when upgrading nightly builds our options get cleared out and have to be reset. Is this sometimes intentional or should it be reported as a bug when found?

Things I reset a lot are severity level related to 'var' suggestions, naming conventions, and once I lost one of my surround with templates (only once 'cause I never replaced it).

Thanks,

Sam