Maybe it would help if you described your procedure by means of an
example. Something like:

I select the entire sheet2 on file1 and do ctrl-c
then I switch to file2, select A1 on sheet2 and do a ctrl-v

When I then look in cell P5 it says

='[Checkout Blank.xls]CHEKOUT5'!$B$3

How can I avoid copying this from sheet2 on file1?

Answer: Empty P5 on sheet2 of file1 before you hit crtl-c

Something along these lines.

Hans