There is a balance to be sort after, if the bike is on a stand and the wheel is off the floor, then the weight of the wheel tends to hold the tops against the top of the forks. If the weight of the bike is on the wheel, then when the threads clear, the suspension collapses and the top shoot up, this can be detrimental to the threads on the tops as they are alloy and can deform as they get to the end of the thread.
I tend to support the bike on a jack stand with the wheel just touching the floor, when I feel the top has cleared the threads in the forks I lower the jack to raise the tops and get at the nut to release them. I also remove the long rods (brass adjuster, take note of which side they come from) from the damper and don't put them back until it is all buttoned up.
None of which seems to be your problem, When you are sure the threads have cleared, try pushing down on the forks.