Hello David,
There will be no compatibility issues at all between the two CD-players. Both are pretty much the same inside (however on the tech side I think there is two diffrent versions of 5500 CD inside). But for use on a Beomaster 5500 there will be no diffrence in use.
There will be a slight diffent outside look of the 6500 since it has polished aluminium panels and compeltely dark topside. You probobly already seen that diffrence.
Usually there is some old caps that have given up that stops the CD 5500 to missbehave, you could search this forum for info since that would be a rather "easy" fix for a person with good solderskills.
Hope this helps
Jesper
Sweden