I have this problem when I place a blueprint with a quality fluid storage or when I just upgrade them from normal to quality that they are not connected anymore but the green cable are still in place but you can connect a new one on top of it.

Are you talking about storage tanks? I just tried to reproduce the issue, and for me circuit wires stayed connected as expected when replacing different qualities, as well as when using an upgrade planner to upgrade from normal to a higher quality.

Using an upgrade planner to upgrade entities of higher quality is much more difficult, since you'd have to select the "qualitised entity" as the correct source entity to be upgraded, but I don't see how that could cause this issue either...

I think it has to do with K2 Fluid Storage (https://mods.factorio.com/mod/k2-fluid-storage) and your mod because there is a duplication issue, you can try yourself place a quality Huge storage like Epic and when you mine it you need to mine it twice and you get 2 of it

also try to put a k2 storage quality connect a green wire with a pole on it copy them and paste them you will get the storage without a green circuit pasted

with a normal tank from base factorio there is no problem tho

it's like when you place the quality storage you forget to remove or it doesn't remove the old one too because when you remove the k2 quality storage it show the old entity behind

This mod has an issue with placing dual entities, particularly affecting tanks, mining drills, and other entities from other mods. When placing an entity, it actually places two entities: the original vanilla entity and the modified entity from this mod. Consequently, mining/harvesting triggers twice, and blueprints become corrupted due to conflicting entity types. Please check the entity replacement logic to ensure complete override instead of duplication.

This is a good point. I assume the issue is other mods changing fast_replaceable_group after this mod generates the "qualitized" entities, but K2 Fluid Storage doesn't seem to do this on its own. I'll have to investigate this, so it would help if you could list some other mods with entities that have the same issue.

A general safety backstop of deleting the original entity if it still exists (and the new one exists as well) probably can't hurt though.

Considering the extensive compatibility required with numerous mods, and to avoid manual troubleshooting for each one, I strongly recommend ​prioritizing the implementation of the safety backstop mechanism​ (deleting the original entity if duplication occurs). This universal solution would resolve the core issue across all affected mods, rather than addressing compatibility case-by-case.

It wouldn't really resolve the issue. If the original entity isn't replaced, it means that the fast replace failed in general, so settings from the ghost/blueprint were not copied over to the newly placed entity. It could even lead to item loss if some other mod inserted something into the original entity before it's destroy-replaced.

It would just trade in one issue for a potentially less problematic one.