Yes.
The way armor penetration works makes every point you have in armor penetration worth more than the last point you put into it. Strength, on the other hand is constant but scales with buffs.
Armor penetration also makes every point you have in strength worth more because it causes each point to translate to higher DPS.
In explanation of your situation, the armor penetration gems you removed cause every point still in armor penetration to be worth less than they were before. Once you get all of them replaced with str gems, your dps will increase because you will have the same number of armor penetration you had in gems in strength now, which is worth about 2x as much as your arp gems.
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