Setting up a systems with two compatible force fields in separate folders

GROMACS version:2021…6
GROMACS modification: No
Dear Gromacs Developers and Users,
I am trying to setup a simulation of a protein-DNA complex. The force-field files for protein and DNA are available separately and they are compatible with each other.
They have a large number of common atom names with slightly different values. If I just merge the files (taking care of the proper sections), I get warnings like this

WARNING 1 [file ffnonbonded.itp, line 90]:
  Atomtype CT was defined previously (e.g. in the forcefield files), and
  has now been defined again. This could happen e.g. if you would use a
  self-contained molecule .itp file that duplicates or replaces the
  contents of the standard force-field files. You should check the contents
  of your files and remove such repetition. If you know you should override
  the previous definition, then you could choose to suppress this warning
  with -maxwarn.

These can’t be ignored because I would have to treat CT atoms in DNA differently than CT atoms in protein.
I think if I rename all the common atoms in either DNA or Protein force field files, it would work. But the number of such atoms is huge. Is there an easier way to handle such cases?
I would be really grateful for any suggestions.