You got it right Jojje.......PW 08.11.11.123 is specifically released for OPM SS5 so it will only come up when you search for OPM SS5 and not in the general search.
PW SS4 Refresh 08.11.11.559 has been released just today but OPM SS5 has not been certified with this version so I would suggest not using it.
In step 3 the file is saved, so it does not mean a copy of this dgn is created, (with File Save As option), right?
After step 4 (the components were checked in), there will be following outcome based on operation:
1. If the leave reference option was not enabled and check in was successful, components will be deleted from dgn file and there will be nothing in dgn file.
2. If the leave reference option was enabled and the check in was successful, components will be retained as reference components in dgn file, you wont be able to edit them.
3. If leave reference option was enabled/disabled and check in failed due to some error, components will be there on server but will not be deleted from dgn file.
If the case is 3 above, then as per Step 5, Free will not do anything but subsequent check in on server will create duplicate GUIDs for piping components.
I suggest you follow up with TSG as you already have logged a ST for this and if this is causing a very big issue for your production version.