my knees hurt after reading all this 
. Wish you all the best in recovery.
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We don’t paddle with knees but we use our thighs to brace and need knees to activate thigh movement. Pillows or other supports under knees in a low volume boat could cause entrapment issues.
OP, you haven’t really said specifically why you can’t use your Avocet. It would be informative to know what exactly the issue is. is it just getting in, is it pain from having to spread your knees once you are in? What specific aspect of your new knees are causing the problem?
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Just wondering if I will be able to bend them enough to enter… I am(was) a butt sitter in the seat then bringing my very bent legs into the cockpit…Hope I’ll still be able for that but I sorta doubt it…
I can’t imagine getting into a kayak that way, even with good knees. Depending on your launch situation you could use the dock, the shore or even a paddle float for support (or a helper) while trying to adapt to a feet first method. Probably lots of practice on dry ground first. If you can’t do it on dry ground its probably time for a new kayak, or a reciprocating saw, but the latter could affect resale value. 
You will want someone nearby even for dry ground practice, b ecause you may need help getting out. I almost got stuck in one of my kayaks in my front yard last summer when my knee was in worse shape. It was tough getting in but almost impossible to get out. This was a low volume skin on frame though.
Once you do get in you may find new troubles, if the Avocet keeps your knees splayed open. I had to sell a very nice low volume stitch and glue last year that forced me to do that because my bad knee simply could not get comfortable in that position.