Just don't know if this is working as intended.

From the game I played, it seems I don't keep to hold on to those systems (which were taken away via influence) right after the truce ended.

This is intended. The rule for Supremacy Victory formulates as "last Empire to keep their home system intact wins". As soon as you lose control of you home, you are blocked from achieving this victory type in particular game, even if you manage to take it back.