After another hour of bashing my head (ouch) I decided to do some more googling (didn't find anything first time round) and this time actually found a good suggestion which worked!!!
To get rid of unwanted links, save the file under the same name as the file it links to. So in my case, I created a new excel file called Link.xls, which was blank, then in the Edit/Links box changed the link to be to this new file called Link.xls. Then all I had to do was Save As and select Link.xls so that it is linked to itself!
Everything seems to be working, all of the calculations are still there, macros work, etc. Hopefully this has sorted the problem.
Thanks anyway, I'm really sorry - I hope I haven't wasted anyone's time!