Steps to recreate the bug:
1. Place a factory near substation with 4 existing wires.
2. Fill that factory floor with something.
3. Place another factory nearby.
4. Get "Max of 5 connections reached" warning.
5. Cut both factories.
6. Place some additional poles.
7. Paste both factories back.
8. Notice that both factories are empty.

Some additional steps:
9. Look around inside factory floor surface, you'll find your old factory floor (blinking with "no power" icons).
10. Teleport there.
11. Walk out (you'll get to where you started - outside one of your newly placed factories).
12. Walk "back" in - you'll get to the empty factory floor.

If you repeat steps 5&7 you'll get yet another new empty factory floor, with the same behavior - if you teleport between them you exit the same factory, but on entry you get only to the newest one.

I couldn't reproduce your issue, but I've put some thought into this and have a theory about why this issue is happening.

In version:1.0.7 I made some changes to saved factory ID numbers. It could be possible that one of the new IDS overlapped with something from the old system, causing an invalid factory.

Can you try to reproduce your issue again in a new sandbox world? It's likely that this is just an artifact of bad migration scripts on my part, and if so then the problem would go away on its own.

You can try /give-lost-factory-buildings to get the old buildings back. If the command doesn't work, send me your save and I can fix it manually.

Reproduced in sandbox with 1.0.10.

Looks like the problem is with "Companion drones" mod I use instead of construction drones. They cut (or deconstruct) factories just fine, but if I try to paste them back they create new factory floors like new factories. Placing factories manually works fine.

/give-lost-factory-buildings does give factories linked to the old factory floors, thank you.

I'll see if I can fix the incompatibility. Thanks for letting me know

Fixed in 1.0.12