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is it ok to swap cases while leaving alpha 8045 attached?

I don't see why not. Just because the processor and heatsink might move around doesn't mean you'll have to clean and reaply the thermal paste.

Depends if it's easier for you to take it off and install it again with the HSF in the way.
 
I think the mounting method of the Alpha makes it way safer to leave on the CPU/MoBo than a "regular" type of HSF that utilizes the 2 plastic clips on the socket. I've heard of people having those clips break off, but you'd have to try pretty hard to knock the Alpha off the way it's bolted down using those 4 studs through the MoBo.
 
Actually, I don't think I could remove my 8045 without removing the motherboard.

The nuts are under the mobo. I couldn't get to them without removing the board from the case.
 
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