Imported keys to electrum
What did you actually import in Electrum? A master privatekey, or a list of private keys? 
In the first case, it could be that your gap limit (i.e. the addresses actively monitored by Electrum) is set too low, so it doesn't see some of your UTXOs. You can check this out :

wallet.gap_limit

Then increase the number you will see, for example if it tells you "20" try something like "50"

wallet.change_gap_limit(50)

wallet.storage.write()

Restart Electrum and see if your balance is back.