some users mailboxes are present both on-prem (Exchange) and Exchange Online (O365). And as a result of this, such affected user sees different emails when logged in either with the on-prem link or with the outlook O365 link. Can such account be merged as one?
That's an unsupported configuration, so there is no "solution" Microsoft offers here. Bulk export/import via the PST ingestion tool or a third-party alternative is probably your best bet.
