I'm unsure if this exact bug has been posted or found, so I am posting it here just in case.

The zygarde assembly appears to be broken in some multi-player servers. The following process has been done in both single player and a server.

1. Launch pixelmon reforged version 7.2.2
2. Catch a Zygarde
3. Save the world/server and update to version 7.3.1
4. Launch pixelmon reforged 7.3.1
5. Spawn in a Zygarde and sacrifice it for 50 cells and 1 core.
6. Use the Reassembly machine to make the original zygarde from version 7.2.2 so it has the Power Construct ability.
7. Engage a wild pokemon for a battle.

Findings for Single Player testing: Zygarde changes into 100% form when it meets the requirements, after battle it keeps the power construct ability but the stats and appearance change back to its normal form.

Multi-player testing: zygarde obtained the Power Construct ability. In battle it changed forms and stats.
After the battle the ability got changed back to Aura Break.

2nd testing phase.
1. Remove all zygardes, zygarde boxes, machines, cores and cells from your inventory and pc.
2. Place 100 cells and 5 cores on the ground in both single and multi-player.
3. Use a Zygardes Cube to gather all cells and cores.
4. Once 100 cells and 5 cores have been collected, right click the reassembly machine.
5. Assemble without zygarde. This should give you a Zygarde with power construct.

Findings on single-player: Zygarde obtained the Power Construct ability and changes form when in battle requirements are met.
Once the battle ended zygarde is returned to its 50% form but will continue to have his power construct ability.

Multi-player findings: Zygarde did not obtain the power construct ability. The 50 additional cells required to turn an aura break zygarde into a Zygarde with power construct have been consumed and are not returned upon separating zygarde.

The issue seems to be server sided, assumptions are either server files or plugins not allowing the change. There are no errors in logs when this happens.