It seems to be the same problem in version Mekanism-1.16.5-10.1.0.455.jar
It is randomly, sometimes the multi block structures are connected and any other are disconnected after restart the server. Is also happens with the "induction casing battery" or "Thermal Evaporation Tower" or "Fusion Reactor" or "wind turbine" or "boiler" .... all multi structures randomly.

And its fixed randomly after Server restart. Before i restarted, the i had fix the left tower by replace on block from the multi block, but the right tower was broken. after restart also the right tower was fixed, although i dont replace a block from the multi block structure.

! To Replace a pipe on the port doesn't fix anythere.

Server java version:
openjdk version "16.0.1" 2021-04-20
OpenJDK Runtime Environment (build 16.0.1+9-Ubuntu-120.04)
OpenJDK 64-Bit Server VM (build 16.0.1+9-Ubuntu-120.04, mixed mode, sharing)

Client java verison:
Java 1.8.0_51 64bit

Minecraft Server version:
mohist-1.16.5-900-server.jar

Modlist:
alexsmobs-1.12.1.jar
appleskin-forge-mc1.16.x-2.2.0.jar
appliedenergistics2-8.4.6.jar
Aquaculture-1.16.5-2.1.21.jar
architectury-1.28.48.jar
BiomesOPlenty-1.16.5-13.1.0.477-universal.jar
blockcarpentry-1.16-0.4.0.jar
Bookshelf-Forge-1.16.5-10.3.29.jar
carryon-1.16.5-1.15.5.22.jar
cfm-7.0.0pre22-1.16.3.jar
cgm-1.1.0-1.16.5.jar
Chisel-MC1.16.5-2.0.1-alpha.4.jar
chiselsandbits-1.0.63.jar
ChunkAnimator-1.16.5-1.2.4.jar
chunkloaders-1.1.7-mc1.16.5.jar
citadel-1.8.1-1.16.5.jar
cloth-config-4.13.49-forge.jar
CodeChickenLib-1.16.5-4.0.6.443-universal.jar
compactmachines-4.0.0-beta.2.jar
CraftTweaker-1.16.5-7.1.2.486.jar
create-mc1.16.5_v0.3.2g.jar
CreativeCore_v2.2.1_mc1.16.5.jar
CTM-MC1.16.1-1.1.2.6.jar
Cucumber-1.16.5-4.1.12.jar
Cyclic-1.16.5-1.5.13.jar
DynamicTrees-1.16.5-0.10.0-Beta26.jar
DynamicTreesBOP-1.16.5-2.0.6.jar
DynamicTreesPlus-1.16.5-0.1.0-Beta10.jar
elevatorid-1.16.5-1.7.13.jar
EnderStorage-1.16.5-2.8.0.168-universal.jar
fishingoverhaul-1.16.5-1.0.2.jar
FluxNetworks-1.16.5-6.1.7.12.jar
flywheel-1.16-0.2.5.jar
gravestone-1.16.5-1.0.6.jar
Hwyla-forge-1.10.11-B78_1.16.2.jar
invtweaks-1.16.4-1.0.1.jar
ItemPhysic_v1.4.18_mc1.16.5.jar
jei-1.16.5-7.7.1.139.jar
JEITweaker-1.16.5-1.1.0.49.jar
JustEnoughResources-1.16.5-0.12.1.133.jar
kotlinforforge-1.16.0-obf.jar
lemonlib-1.3.6.jar
Mantle-1.16.5-1.6.152.jar
Mekanism-1.16.5-10.1.1.456.jar
MekanismAdditions-1.16.5-10.1.1.456.jar
MekanismGenerators-1.16.5-10.1.1.456.jar
morecfm-1.3.1-1.16.3.jar
Morpheus-1.16.5-4.2.70.jar
MouseTweaks-2.14-mc1.16.2.jar
MysticalAgriculture-1.16.5-4.2.6.jar
obfuscate-0.6.2-1.16.3.jar
OreExcavation-1.8.157.jar
simplegens-1.16.5-3.0.9.2.jar
Space-BossTools-1.16.5-5.5e.jar
StorageDrawers-1.16.3-8.5.0.jar
supermartijn642configlib-1.0.9-mc1.16.jar
TConstruct-1.16.5-3.3.2.324.jar
TravelersBackpack-1.16.5-5.4.5.jar
valkyrielib-1.16.5-3.0.9.5.jar
vehicle-mod-0.45.2-1.16.3.jar
WailaHarvestability-mc1.16.x-forge-1.1.15.jar
WAWLA-1.16.5-8.0.1.jar
Xaeros_Minimap_21.23.0_Forge_1.16.5.jar
XaerosWorldMap_1.19.0_Forge_1.16.5.jar
xlfoodmod-1.16.4-1.2.0.jar

Not this again

I understand it could have been that it might be immediately clear what the reason might be.

Never happened to me on server. Some people having this issue have mohist, and mohist isn't very stable with some mods... Have to check if other people have this issue too, and if yes, if they have mohist. Maybe this is related, maybe not. Maybe it's caused by another mod, maybe not... very hard to know, there is no way to reproduce it, no logs, nothing...

It happens frequently for you ?

Try without Mohist, but also this seems relatively similar to #6356 so just closing this and merging it into that unless there is something about it that is different that I am missing, in which case please say what it is and I will reopen it.