Okay I'll admit I'm confused
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If the wheelbase has shortened and the distance from hub to headset has shortened then that would have made me think that the old fork was a (more) curved one, like an old steel one that placed the front wheel further forward. That would mean a straighter (new carbon) fork has a steeper rake and hence shortened the wheelbase. This will alter the geometry and handling, although maybe for the better. Old curver forks tended to give a more twitchy front end that the more current straighter fork which gives a more stable and direct front end. Too steeper angle though and it would go the other way with you being too far over the front wheel.
Mentioning an integrated headset makes me think that it's not an old steel frame though, but some aluminium frames came with aluminium forks which were more curved than carbon ones. My Dad's bike (before I gave him my old frame) for example came with an alu fork, he changed this to a carbon one later and did comment on improved handling.
An easy check is to hold the old fork alongside the new one and match at the headset and see if it's an increased curve/rake over the new one. If the old fork has a bit more of a curve and the wheelbase has only been shortened by 2mm than my guess without seeing it would be as I mention above and the handling will probably be improved and a bit more stable at the front. To give a simple check ride no handed and see if it feels more stable than no handed before.
All that said it shouldn't lower the front end at all. You didn't take a space out from under the stem at the same time did you
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