Firstly, it is never a good idea to save a file over an existing one but drawings are normally the least problematic.
Secondly, it can be done but with care...
After you have checked out the files and 'replaced' the drawings and BEFORE you check then in correct the files properties. This is done by using the EPDM command from the explorer window "Modify -> Update -> File Attributes from Database".
This will only update the Drawings with the information that is on the datacard. Any properties that you do not store on the datacard needs to be corrected in the drawings manually.
That did the trick, appreciate it.