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You can remove all backup records from the database at backup time. Go to Akeeba Backup. Select the backup profile you are interested in. Go to Database Tables Exclusion. Find the #__akeebabackup_backups table and click the second icon ("Do not backup its contents") to make it active (yellow / orange background). This will back up the table structure so that Akeeba Backup can still work, but leave out the backup records so you don't see them on the new instances.

Side note: If I remember correctly the latest backup, the one you are currently taking, will still be included in the backup archive. Please note that this is off the top of my head, I have not looked at the code to confirm this, and it's been quite a while since I last refactored that code.

You can do that for #__akeebabackup_profiles, though the first time you launch Akeeba Backup on the new instance it might show an error because it expected the default backup profile (id 1) and found none. However, when this happens we also save the default, factory-reset configuration state as the default backup profile which should mean that reloading the page will now let Akeeba Backup work.

With these two changes you will effectively have the equivalent of a brand new installation of Akeeba Backup on your new instance.

You can delete all backup records with TRUNCATE TABLE #__akeebabackup_backups where #__ is the table name prefix of the site.

If you have newer backups, use phpMyAdmin (or something similar) to see the contents of that table, and delete the older records. I wouldn't know how to find them, as "older records" is very much dependent on when you restored the site and when you took a new backup.

You can of course just log into your site, go to Akeeba Backup, Manage Backups, select the older records and click on Actions, Delete. It is directly equivalent to managing the database table directly.

There are similarly named actions in the Actions drop-down: Delete Files and Delete. You must use the latter (Delete), right at the bottom of the Actions drop-down. Their difference is documented.

Delete Files only deletes locally stored files associated with the backup record. This is an obsolete record. An obsolete record is a record which does not have any locally or remotely stored files associated with it. Therefore, by definition, Delete Files will have no effect on it.

Delete removes the backup record itself. If there are locally stored files associated with it Akeeba Backup will perform a Delete Files on it, then delete the database record. If there are no locally stored files associated with it Akeeba Backup will just delete the database record.

I know this works as I am using it on a daily basis. Developing this software means that I may run dozens of backups in a short period of time. I don't enjoy having a thousand junk records in the database; I select them when I am done working on the backup engine and click on Delete. I actually did that just twenty minutes before this reply, and it of course worked :)

No worries! We've all made that exact mistake – even those of us who should really know better :)