Are you accessing the FDM Web Server Directly are accessing via a load balanced URL? - Test the process locally on the server using http://localhost/hyperionFDM. If it is working locally on the server properly with "localhost", it would indicate a network or load balance server issue.
Also The default timeout for IE would be 60 minutes. If you run the same process locally on the FDM Web Server itself do you see the same behavior?
Also which broswer are you using ??
Please confirm .
as your issue is related to clearing data before loading (replace mode), I would suggest you to log in a file the clear scripts being executed (comment fcalculate line so scripts are not executed). The create CSc in essbase to run the clear scripts from essbase and see results.
you can write clear scripts and comment line in LOAD ACTION SCRIPT (expand essbase adapter > actions > double click LOAD)