I think the best method is case by case, but appreciate this creates another workload.
Wanted markers should of course clear, but IRL other intelligence markers have a period of time they can be removed and others that are quite serious remain permenantly. I've not seen the PNC system here to see how warnings display, but if not already a date should display next to the marker for when it was last relevent. Eg if the last time you were seen with a firearm in a concerning manner was March 2019 then the marker should date March 2019. If then today you commit to another incident with a gun then the Firearm warning should list todays date.
This way the marker remains for the lifetime of the record, but if they have behaved for some time you can quickly see the person hasn't done anything to trigger a warning for 2 years if looking at above example.