try this:
@echo off &setlocal
set "folderA=D:\NONMEM7.3beta7.0"
set "folderB=D:\NONMEM7.3beta7.0Renamed"
for %%a in ("%folderA%\*.f90") do if not exist "%folderB%\%%~na_recoded%%~xa" echo %%~na_recoded%%~xa not found in %folderB%.
for %%a in ("%folderB%\*.f90") do for /f "delims=_" %%b in ("%%~na") do if not exist "%folderA%\%%~b%%~xa" echo %%~b%%~xa not found in %folderA%.