absolutely not possible, sorry.
at least not by deleting nothing but the
ini files from the mentioned folder -
they store the info on your personal preferences and similar stuff.
they got nothing to do with quests.
did you delete/change something else?
how come you only noticing that now?
(maybe you just went back to some earlier save before changing to Enderal?)
EDIT
when starting Enderal at first you tried loading a Skyrim save, right?
according to the pinned
Support-Topic
saves could get corrupted when loaded in the wrong game.
(don't know how that would show)
so
is the save from which you lost your progress the one you tried to load in Enderal?
that could be the reason.