When a ROMS config is first run it is typically done so with an initial condition file ININAME and nrrec=0
https://www.myroms.org/wiki/roms.in#Output_Frequency_Parameters
https://www.myroms.org/wiki/roms.in#Input_NetCDF_Files
Subsequent runs usually require setting nrrec=-1 and ININAME == roms_rst.nc (assuming RSTNAME == roms_rst.nc).
Currently the changes above need to be done manually. This logic could be added to the driver, to do it automatically when a restart file is found. Similar logic is present in the cice model driver
https://github.com/payu-org/payu/blob/master/payu/models/cice.py#L181-L186
The biggest issue is that the ROMS standard input script does not use a standard format for which a parser is available, so modifying values in-place would be more difficult and error prone.