According to the Pixelmon wiki, if a pokemon forgets an egg move that was bred on to it, the Move Relearner should be able to reteach the forgotten egg move:
https://pixelmonmod.com/wiki/index.php? ... _Relearner

However, this is not the case. If an egg move is forgotten, and the pokemon cannot learn said move by level up, the relearner cannot reteach this move.

Here is an example of how to reproduce this bug.
1. Give yourself a Hitmonchan whose level is at least 16.
2. Teach it the move Bullet Punch if it does not already know this move. This can be done via the Poke-editor or the Move Relearner since Bullet Punch is a level-up move for Hitmonchan at level 16.
3. After Hitmonchan knows Bullet Punch, have it forget any other moves.
4. Breed this Hitmonchan with a Ditto and hatch the subsequent Tyrogue Egg. Bullet Punch is an egg move for Tyrogue but not a level-up move.
5. Now, either delete Bullet Punch from Tyrogue or replace it with another move.
6. Interact with a Move Relearner and select this Tyrogue.
7. Notice how Bullet Punch does not show up as a move that this Tyrogue can relearn.

Apologies for leaving this ticket behind. I was able to reproduce the issue on the latest version.
There is a pending ticket with the same version. It is quite old though so I'll make sure to remind the rest of the team about it. Still marking this one as duplicate though.
Original ticket: https://www.pixelmonmod.com/tracker.php?p=2&t=13425