We were migrating some complex databases via syncing the contents and found the following error with MySQL sartup on destination system, after the sync is completed

[ERROR] Plugin ‘InnoDB’ init function returned error.
[ERROR] Plugin ‘InnoDB’ registration as a STORAGE ENGINE failed.

To fix it, we have removed ib_logfile0 and ib_logfile1 from the destination server and that fixed the issue.