Hi Bobinor and welcome to the Ford Fusion Club. Unfortunately yes, if you still get flickering after reinstalling the halogen bulbs, there is probably damage to the lighting/electrical system.
Normally troubleshooting (and overall advice) would be to reinstall the halogen bulbs. However, since you already did that and the problem is still present, further troubleshooting will need to be performed by a shop, unless you have the tools to do it.
Let us know how you make out and good luck.