Well, if these are really thousands of copies of (nearly) the same e-mail, just search for something that's in these e-mails (but not in others). Then, in the list of found messages, select all-but-one of them and delete them.
edit: Oh wait - never mind. You have thousands of e-mails that each have one duplicate. Yes, that complicates things
The "Delete Duplicates" item of the "Folder" menu compares messages within a folder and delete duplicates. Messages are considered duplicates if their "From", "To", "Message-ID" and "Date" attributes are equal, even if other parts are different. Sometimes it happens that messages have differences in one or two of the above attributes, but are otherwise identical, so it is worth excluding some of the attributes from comparison.This happened in your case while time is different by a few hours, most probably because of invalid time zone configuration on one or more computers with which you synchronize messages.
The Bat! version 7.4.4 offers more options for deleting duplicate emails. This version introduces new command line parameters to exclude certain attributes from comparison when deleting duplicates. So, you can exclude message creation date/time. For more information on command line parameters supported by The Bat!, their usage and samples please refer to https://www.ritlabs.com/en/support/help/77/#6680
Since you wrote that during backup/restore a time shift in a few hours appear in message, one possibility of this problem is that one of the computers that take part in synchronization (or backup/restore) don't have time zone information set correctly while The Bat! keeps message dates in UTC (Universal Time Coordinated). If the time zone is not set correctly, then The Bat! is unable to calculate UTC message date/time correctly. To make sure that your computer have correct time configuration: (1) make sure that time zone is correctly set in Windows "date and time settings"; (2) synchronize time over internet, never update time manually, and after you have synchronized time over internet - please check whether time in Windows shows correct time after synchronization - and if it shows correct time, then The Bat! will calculate UTC properly.