Hi peggyprentice,
Looking at the problem is a pragmatic step toward solving it. But Sherlock Holmes taught us that logical deduction also leads to knowledge. So, here goes:
A hyperlink to another workbook contains a path, say, "C:\My Documents\This subject\myfile.xls". Now, if you were to save a file from where this address isn't accessible the link would be "lost". Pragmaticism requires that we look at your code but in the light of the above (Holmes) I doubt that we will find the solution there. You may be quicker by examining how the change of file name and location affects the missing links.
In other words, it isn't, most probably, the Paste Special that is causing the problem but the SaveAs. And it shouldn't be the SaveAs command that is causing the problem but the relative change of names and locations vis-a-vis the hyperlinked files. We may not find this in the code.
As for the conditional formatting, King Solomon might say that it is either related or it is not. Again, we may not be able to tell by what you post. But you should be able to tell pretty quick if the conditions are somehow affected by the hyperlinked data that suddenly turn up missing. My suggestion is to ignore this subject until the hyperlinks problem has been solved. If, then, it turns out not to be related, meaning it didn't go away by itself, post the problem in a separate thread.
Have a great weekend!
Have a great day!
Sisyphus
I do this for "honour and country" - much less of the latter, actually.
If I helped you, award points, plenty of them.
If I bored you, deduct points for being too long-winded. (I know, :lol)