I'm playing 1.20.1 bigger reactors in a custom modpack of mine so it could be that but every once in a while the reactor will disassemble then reassemble itself causing the loss of all my fuel, also you can see it happen in real time its only a split second you could see it.

This type of issue is extremely hard to debug. In order for me to fix it, you will need to find some pattern with when it happens. Most commonly this is around a chunk load/unload. Once a pattern is found where I can reproduce the issue, I will be able to fix it.

I'm having the same issue in an all the mods 9 to the skies world, to replicate, turn on the reactor at any power level, fly out of render distance, fly back, reactor will reform as you get close, even though ftb chunks is set to force load that area

Able to reproduce the reactor shutting itself off, unable to reproduce fuel loss. Notable, the reactor reforming is actually correct behavior, the multiblock itself is reformed every time the chunks are reloaded (on the server). Having the reactor's chunks force loaded did prevent the issue i reproduced (reactor disabling itself) with when chunk force loading was disabled.