Eclipse fails to start after some manipulations of plugins

I suspect that I discovered a p2 issue that affects the Flatpak distribution of Eclipse. Doing some steps can break the installation and it cannot be repaired even using "-clean" argument, at least this is what happens in my case. I suspect this is a p2 problem so I've filed the issue there. Please see the referred issue for more details:
https://github.com/eclipse-equinox/p2/issues/555

Perhaps others can try the outlined steps and confirm that the issue is reproducible.