You can transfer the custom directory without changing anything.
Procedure
Open Windows Explorer and go to the directory <PPM_CURRENT_DATA>/custom/<client>.
Delete the config, xml, and data directories.
Switch to the <PPM_PREVIOUS_DATA>/custom/<client> directory.
Copy all directories from this directory to the clipboard except for the bat, config, log, and patch directories.
Now go to the directory <PPM_CURRENT_DATA>/custom/<client> and paste the copied files.
Note that <PPM_CURRENT_DATA>/custom/<client>/xml/<client>_CTK.xml contains the current settings of current PPM version including, for example, descriptions of batch files, which were added in the new PPM version. Therefore we recommend the backing up of this file for a later merge.