The action of adding additional items to an existing stack of stackable or mergeable (percentages types) items contained within a container type (crate/bag/etc) does not reset the persistence timer of the container as would be expected...
This was found in game to impact bags but should impact any container type.
In my test I used bullets as my stackable type. I suspect all stackable types to behave the same.
I also found percentage based "mergeables" have the same issue (i.e. stacking/merging/combning quantities of alcoholic tincture OR iodine and other similar types
Note that I adjusted the persistence time of the bag I tested with as well as the item clean up distance to make testing easy. This will occur at the default values as well.
Link to unlisted Youtube Video demonstrating the issue in detail with stackables:
Detailed Persistence Test