Does an ad hoc, full backup, using Oracle RMAN, flag files, so they are not backed up by the regular backup?
Overview of Backup Optimization


  When you enable backup optimization, the BACKUP command skips backing
  up files when the identical file has been backed up to the specified
  device type.
  
  ...
  
  RMAN uses backup optimization when the following conditions are true:
  
  
  The CONFIGURE BACKUP OPTIMIZATION ON command has been run to enable backup optimization.
  You run BACKUP DATABASE, BACKUP ARCHIVELOG with ALL or LIKE options, or BACKUP BACKUPSET ALL, BACKUP RECOVERY AREA, BACKUP RECOVERY FILES,
  or BACKUP DATAFILECOPY.
  Only one type of channel is allocated, do not mix disk and SBT channels in the same backup command.
  


With backup optimization, the database will not backup the same, identical file more than once to the same device type.

Other than that, the files will be backed up by the regular backup as well.