MOM_interface/cime_config/buildnml lines 403-405 check for the existence of the MOM6 restart file
for a single instance; ${CASE}.mom6.r.${DATE}.nc, even when it's a multi-instance case.
It fails in that case because the necessary restart files have the instance numbers in them:
${CASE}.mom6.r.${DATE}._${INST}.nc (old, default form) or
${CASE}.mom6_${INST}.r.${DATE}.nc (new form).
I suggest that the check for restart file(s) be put into the if-blocks earlier in the function.
I don't know the right combinations of testcase, run_type, continue_run, inst_suffixes, etc.
to use in the conditionals, so I don't have a proposed improved function.