I understand you correct that Mycelium Gear derived different addresses from the Electrum xpub key than Electrum did?
Which addresses to you get when you use this homepage:
https://bitcore.io/playground/#/hdkeys ? Elecrum or Mycelium Gear?
Electrum only supports the first/default wallet/account of the in BIP32 described HD wallets.
See here:
https://github.com/bitcoin/bips/blob/master/bip-0032.mediawikiCould it be that Mycelium Gear used another wallet than the default one, thus you don't see the addresses in Electrum?
Edit:
I found
https://github.com/vbuterin/pybitcointools.
Maybe you could use this tool to get the private keys of the addresses your customers have paid to and import them individually.
From what I understand Electrum is not BIP39 compatible that is why the Electrum seed phrase does not work in MyCelium.
But because Electrum is BIP32 compatible once you have the master seed (which is derived from the seed phrase) it should be compatible with any BIP32 wallet app, as long as they support the import of this master seed.
In the following BIP32 picture the master seed is described as master node and the seed phrase as master seed: https://github.com/bitcoin/bips/blob/master/bip-0032/derivation.pngThere are also some commits that have not been merged to the master yet that might be interesting to you:
https://github.com/vbuterin/pybitcointools/pull/84/commits