I have a ledger nano S where i keep some funds on, and in order to send and receive easily (before they developed the x version) i installed a coinomi wallet on my phone using the same seed. So far so good. Sometimes i purchase stuff and send with coinomi: all great.
NO! NOT "great"!!?!?!
Regardless of what happens with your Digibyte... you should
NOT have your hardware wallet seed in an "online" wallet... and certainly not in a closed source mobile device wallet!!!
You have effectively removed
ALL the security of the Hardware Wallet by importing that seed into another (non-hardware) wallet!
That seed should be considered compromised and you should immediate create a new seed on your Nano S (wipe it and set it up from scratch as a 'new' device), and then move all the funds from your old wallets to the new one.
Now, the main question would be: how do i get my DGB safe from my coinomi wallet?
It sounds like the Coinomi wallet has used a different derivation path or something for your DGB if they are not showing up in Ledger Live after Ledger Live is synced. Either that, or there is an issue with the Ledger Live sync if it is showing "some" of your Coinomi DGB history, but not all of it.
Perhaps remove the account from Ledger Live and try setting it up again to see if it resyncs properly. Otherwise, if Coinomi is refusing to send your DGB, then I guess you need to find another DGB wallet that supports BIP39 seeds. Unfortunately, I can't help you with that
But, in my opinion, your priority should really be (re)securing all your funds on your hardware wallet!