Ok, so you have to understand that as we don't know exactly what was done, I can only speculate and offer possibilities / suggestions.
I don't know if the engine ECU was reconfigured or had a specific map applied that has deleted specific options.
If the engine ECU was rec0nfigured, it may be a matter of locating changes and reconfiguring these to the factory defaults for your specific engine (this is not going to be easy if you don't know what was there int he first place - these are usually configured via PSA servers specifically to the vehicle with correct parameters at the factory.
Second, if there has been a specific 'map' applied to the ECU, then this may have wiped out certain options, so they may not even by visible.
If this was me (and of course I'd never of have anything like this done in the first place

), I'd personally ask my dealer to re-download the engine ECU software, which should update the ECU with the correct parameters as it had at factory. They'd charge a diagnostic fee of course as they would need to manually check the download has been applied, but this may be the easiest way to restore the factory options and eliminate guesswork.
As far as regeneration goes, 'passive' regeneration is just that - if you are driving on a motorway for example and the exhaust gasses are 550 °C then the particle filter will automatically burn off the particulate matter without the need for any assistance. It's just the assisted element that relies on the engine ECU being able to do its job. So for assisted DPF functionality to work, the additive pump need to be present, configured and working, as a minimum, otherwise it will not be doing the fuel tank.
Of course the SCR features require a lot more configuration - the NOx sensor (s), Urea pump, Urea injection and tank operations for example - and these may be missing or 'deleted'.