A "uncheck all" button for temp bonuses...
Or define temp bonuses but save whether they are active...
Better would be to save if they are active.
Best might be an option like this: normally active, normally inactive.
For example, a worn ring is normally active, a familiar at arm's length might normally be active.
But Bull Strength would normally be inactive. And ability damage is definitely normally inactive... being something you work to get rid of.
I agree we need a smarter solution. I'd prefer if the on/off state was part of the save. Reload, active ones are still active, inactive are still inactive. That seems to be the simplest and easiest solution. I'd also vote for an ALL ON/ALL OFF checkbox for an easier user experience.