Steps to reproduce:

1. Create a LLD rule where in item prototypes applications are created from prototypes. Check that Keep lost resources period is not 0. (Take e.g. Template OS Linux -> Network interface discovery -> add ‍{#IFNAME}‍ in application prototypes)
2. Let the LLD discover the items and check that new applications are created from prototypes (e.g. in global regular expressions allow lo interface to be discovered, check that in applications now items belong to discovered application)
3. Make the items not discovered anymore and wait for LLD to pick this up.
4. Check the application prototype still exists but does not contain any items. In items they will be removed as per LLD settings but applications are removed from items immediately.

This behavior seems to be misleading, the items should be left with applications till LLD removes both altogether.