Don't worry too much about this.
The Schengen system has not changed. When you notify and travel, an alert is placed against your name/passport on the Schengen information system (SISII). When you enter a schengen zone country and they swipe your passport, it does an online check and will flag up to the border guard. If the border guard has seen a similar alert. he/she will take a couple of minutes to check where you are going and who you are travelling with. If he/she hasn't seen such an alert, they will take a few more minutes reading all the instructions on their screen.
Note that this is an alert for a 'Discreet Check'. It does not deny you entry and it does not have any details about your offence.
In many of the southern European countries, especially during busy holiday periods, passports are often given a cursory glance and not scanned. Even when they are scanned, the don't always have the full online checks 'turned on'. I suspect what has happened in Greece is that their immigration authorities have now made it mandatory for their border to run the full SISII checks. Of course, many of the guards are now seeing these for the first time - they are meant to discretely check where you are travelling to/from and with whom. Taking photocopies happens sometimes, but not usually.
The alert can be seen by all schengen countries but, as I said, it is an alert for a 'discreet check' and has no other information about you or your offence. It's a joke of a system as it is never discreet!
These alerts are time stamped and expire. Once you are off the SOR, they will not be visible on SISII any more - you do not need to do anything, although can always ask your PPU to confirm they have removed them all.
SISII will have the alert information in its archived records for x years, but they cannot be accessed online during normal immigration work and there are tight controls about access to historical records.