I've just tried to replicate this issue, but not being able to.
I'm assuming the pages you are moving between documents do not contain threaded text frames. And for the Hyperlinks that I tested I made sure that 'shared destination' was disabled. When I move pages between two documents the hyperlinks remained in tact.
Tested in InDesign CC 126.96.36.199 on Mac OSX 10.8.4
is there a way to share these documents - so you or anyone can see what is going on?
You can share them on dropbox or other platform and provide a link here if you want people to review the files for you Notannhavoc.
ok - here is a link to the folder
there are 4 files - 2 jpgs - one good and one bad showing hte link - I have also included the indesign fiels but have stripped the pages in the file to jsut one spread . You will see that all teh hyperlinks remain even though the pages are gone - however ethy are greyed out - the active ones are black. In the test-bad file they hyperlnks point to somethign completey different.