Considering that you already have Entra Connect in place - there is no need to "bypass" it. If you want to configure all currently synchronized users to cloud only users, follow https://zcusa.951200.xyz/en-us/answers/questions/843619/convert-on-prem-ad-connect-synched-users-to-cloud
If mailboxes are hosted elsewhere (e.g., on-premises Exchange or third-party services), you'll need to migrate them:
- Use the Microsoft 365 Exchange Admin Center for mailbox migration (e.g., cutover, staged, or hybrid migration).
- If mailboxes are already in Microsoft 365, no migration is needed—verify they’re properly accessible post-sync removal.
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hth
Marcin