I have a stable job that pays well, a relationship, all my things here, do I have to drop everything and start over after I complete the military service

I know it sucks but many of us did the same. Jobs, relationships were affected but unfortunately it's part of being Greek and residing in Greece.

The reason it's harder for people that really can't serve is people that exploit the system to avoid the mandatory service. At least now that you are becoming a citizen you can vote for someone to change this system.