Hi.
I have a FTB Revelation v2.5 server and something interesting happened with the flux networks, I will try to explain it, even though my English is very bad.
In The End dimension, a user configured a plux point together with some machines to recharge power wirelessly (enderIO).
Then there was the need to restart that dimension, so the server was stopped and the "DIM1" folder of the current world was deleted.
After the server was turned on, a new dimension was generated and everything seemed to work normally, but when users started to enter the server, most reported that their private and public flux networks had been removed and had to be reconfigured.
I am not sure what caused that failure, but I have a theory, and it seems that that flux point that existed in The End caused that all the information of the existing networks in the server was restarted, perhaps because that world of brutal form.
I expose this situation so that it confirms if I am right, and if so, make the necessary changes so that the data of the networks is not eliminated when there is "inconsistency" like this in the registers.
If you need more information, let me know and I will provide what is necessary.

Forge 14.23.4.2759
fluxnetworks-1.12.2-3.0.16-11.jar
spongeforge-1.12.2-2768-7.1.3-RC3496.jar

regards!

I've been noticing this too, but it doesn't seem to be related to any worlds being deleted. At random it seems like it just wipes the entire server's networks. I'm thinking it may be related to not properly saving after a crash (the crash is from an AE2 bug, seems unrelated), since directly after a crash all networks got wiped. It might also be related to a server getting force stopped and not saving the file properly.

It's happened around 3 times for us so far, I don't know how to reliably reproduce it as of this moment.

Minecraft: 1.12.2
SpongeAPI: 7.1.0-4f54ce0d
Sponge: 1.12.2-7.1.5-SNAPSHOT
SpongeForge: 1.12.2-2768-7.1.5-RC3506
Minecraft Forge: 14.23.5.2768

Network data is not stored in any particular dimension. There may be another reason for the issue you experienced this but unless you also deleted the 'data' folder containing the "sonar.flux.networks.configurations.dat" file this wouldn't have been the cause.