Likely because you deleted the objects from the AWS console. In the future you should only remove backup information from the storage tab within the agent. That way we can update the local database with the deletes. Because you deleted in the cloud, the product is unaware of the object deletion, and you'll need to re-synchronize the repository so the product knows about the removal of those objects from AWS. Thanks.

In the future you should only remove backup information from the storage tab within the agent

Just to confirm: There is no way to correctly delete the folder from anywhere in the MSP console, correct?

I'll have to double check, but I believe that's the case. You would have to do it from the agent either on site or by remoting in.

Alternative approach:
We do not allow deletion of storage at the client MSP360 console as a hacker can delete your backups when installing ransomware. It is a setting in the Advanced Branding. It actually happened to one of our clients - the hacker installed ransomware and deleted backups, but fortunately they failed to remove all THREE of our backup copies (One Local, two cloud). After dodging that howitzer, we disabled deleteion of backups from the console and instead use Cloudberry Explorer (or the Backblaze Portal), then we run a repository sync on the client to update the storage usage.
Yes the repository syncs take a long time, and unfortunately no backups can run until repo syncs are complete.
It would be great to separate the repo syncs such that for example, we could still run a local backup while the Amazon repository sync is in process.
And if all that seems like too much trouble, and you want to use the console to delete backups as David suggest, please be sure that you have an MBS console password set , including CLI, and that it is different than the server password.