Not sure if that makes sense
Not really, lol.
When you say you open the hardware wallet with Electrum, are you opening the 2-of-3 multi-sig wallet that we are discussing here? Or are you just opening a standard single sig wallet with your hardware wallet connected?
If you are opening Electrum on its own and seeing one balance, and opening Electrum with the hardware wallet attached and seeing a different balance, then you are opening two different wallets. You will never be able to sign a transaction from a multi-sig doing this. You should be opening the same wallet in both situations.