To reproduce:
-Two Warp Pads.
-One on Earth and one on Mars.
-Link to each other with Warper Cores
-Warp a few times
-Stop server
-Start server
-Crouch and right click on either warp pad

You will see that the Warper Cores have disappeared from the warp pad inventory

This also affects the battery slot of the Warp Pad

This can be reproduced in singleplayer as well.

https://www.minecraftforum.net/forums/mapping-and-modding-java-edition/minecraft-mods/modification-development/2694659-tile-entity-inventory-resets-on-world-reload

Looks like an identical issue

Cannot reproduce on Beta version, probably you are using legacy.