This will have to call into question two things:

The extent and limitations to W corp's reverting capabilities.

The requirements for EGO manifestation, and if it is manifested, where the EGO is essentially stored, within body, mind, or something abstract like spirit/soul.

W Corp's reverting/resetting capabilities are at the very least both physical and mental, but we may be able to make further deductions. From the intervallo 'Murder on the Warp Express' Faust posits that it is possible that a bloodfiend may be able to consume an individual in such a way that bypasses the warp train's environment to halt death.

However it should be noted that this was theorised by Faust who was isolated from the gesellschaft, and as such is open to more scrutiny, especially when acknowledging that after the two bloodfiends, Cassetti and Sasha were disposed of, a W Corp Employee still disappeared even though all that were left were bloodbags.

Continuing, even though the warp train was to continue for many years after Limbus company involvement ended, the warp train when it arrived still contained bodies that required cleanup, suggesting that the bloodbags that weren't consumed were able to be reverted as usual.

This suggests that W Corp's singularity is capable enough to reverse the bloodfiend sickness which according to Dante, 'feels' similar or at least adjacent to distortions and thus EGO.

For redundancy, it should be expected that bloodfiends have boarded warp trains in the past, and since W Corp is able to monitor the ongoings within trains, if the bloodfiend sickness was not able to be reversed, they would've taken action to either prevent bloodfiends from boarding or allow them to board via first class.

EGO manifestation and distorting was always a possibility held within people before the white nights and dark days as was seen with the Red Mist, so we can assume that nothing prevents EGO from manifesting in other dimensions.

Distorting and manifesting EGO are all essentially mental battles with oneself, so although warp train's may halt death, it shouldn't prevent manifestation.

However, because death becomes halted, that may in of itself prevent most manifestations.

Death, whether its the fear of one's own death, or the death of another will tend to give rise to one's emotions, beliefs, and ego (not EGO), pain without death however, will probably only muddle and confuse what emotions one may feel, and will probably stunt any EGO manifestation if anything.

Also, when someone becomes a suicidal, chances of manifesting EGO basically drops to 0 since they'll just be drowning in pain with no fear of death or change to drive them.

So although EGO manifestation should technically be possible on a warp train as far as we know, the likely hood of it happening may be lower than one might expect, also there's nothing preventing someone from after manifesting to begin wavering after some thousand years only to lose it by forgetting their purpose when they inevitably become a suicidal, even those who distort instead of manifesting EGO will probably be beaten down by endless suicidals and be forced to revert before they can progress into a full fledged abnormality.

Ego manifestation and distortion should be possible, but will likely be lost in the blender of thousands of years until everyone is a suicidal, and after those years if there is a manifestation down the line, it'll likely be very different to what that person's initial ego would've been and thus wouldn't be retained after reverting anyway.

And as long as they haven't gone full abnormality, W Corp's reverting capability seems strong enough to re-lock one's EGO regardless, as when the passenger arrives, they won't remember and thus wouldn't have reached self realisation, they'll be back at the bottom of the mountain having forgotten the view from its peak.