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I just switched from a UGF to a canister in my 55. The process was pretty painless, albeit messy. Yes, the plate will need removed. otherwise, you'll have that dead space of water under the gravel going stagnant and potentially creating anaerobic pockets of gas, which will slowly leach through and poison the fish.
If your tank has two plates, remove a half at a time, with a week or two in between. If it's a single plate, sweep the gravel as good as you can before removing, do a quick search here for timandkarens shop vac trick to clean before you pull it. that way you're removing any gunk trapped under the plate before you start digging. It will set off a mini-cycle, but since you said the tank is still cycling, it shouldn't be a terrible set back.
Sorry that's not better news, but, better that than you not removing it and having bigger problems down the line.
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