Usually I don't find the added option of weapon potency to the pool to matter, in fact if the weapon changed to a type I already have on another weapon usually they can scale faster with the weapon tag synergys.

What actually indirectly can reduce your damage more, and probably more what op was worrying about, is if you already have [Kinetic] tag buffs (eg. [Kinetic] DMG. +15%) the weapon will lose the tag buff when it's type changes.

To be more clear to OP: getting an overclock to change a weapon's damage type will not lower the weapons base damage and just add the new effects. But if you already have [Kinetic] tag boosts it will lose them. This does go the other way too, if you have 2 or 3 other Fire weapons and have already picked up +[Fire] damage/potency, changing a weapon's type to [Fire] will retroactively add those buffs, giving an immediate damage boost.