Set the vanilla flint as parent to your custom flint - all child classes are usable the same way as their parents unless specified otherwise, and it will work in all recipes.
You might also want to remap your mod flint to the basic one instead. Remap only activates upon spawning an item/actor and switches them out.
i hope i understand you correctly.
so i double clicked the PrimalItemResource_Flint_mod and chose File ->Reparent Blueprint. then i chose the vanilla flint.
in the primalGameDataBP under Remap Resource Components its set from Flint to Flint_mod.
unfortunately this did NOT work…