You'll still have it.
Let's say you add Mod X that adds Dungeon Y which contains Items Z, A, & B which can all be found in the original game, and you also find Item C, which has been introduced in the mod. Then Z, A, B, & C are required to synth Item D which was in the original game, but has altered statistics whether because of Mod X or another mod.
You will keep Item D, and its stats will revert to the original pre-mod status, just as you would keep Z, A, & B, but not C because C was introduced by the mod, not the vanilla game. Same with if you used any of those items to create an Item F which was introduced by the mod, Item F will be removed upon uninstallation of the mod.
Does that help?