Hello Gregory,
Indeed, if you activate COMPUTATION CONTINUED = YES, even if you add a user_corfon subroutine, with standard TELEMAC-2D, it will not be taken into account.
What you can do is to remove BOTTOM from your PREVIOUS COMPUTATION FILE.
To do so (if not following what is written in the TELEMAC-2D user manual), you can use run_telfile.py Python script with argument alter and option --vars (see the help run_telfile.py -h), e.g.:
run_telfile.py alter --vars 'VELOCITY U,VELOCITY V,FREE SURFACE' input_file output_file
Be careful as the velocity may not fit your new bottom elevation field.
Hope this helps,
Chi-Tuan