Hello Catherine,
This is interesting, I want to immediately say that its sounds like you are hitting the max number of configurations you can have which is 50 but that doesn't seem right. I also took a look at our limits documentation and cannot see anything. If you are getting this error after a small number of versions then I would recommend opening a case with product support to look into it as well.
As for deletion you cannot delete individual versions of the messenger configuration, only the entire messenger configuration. I don't see an ideas in our portal either so this might be a good feature enhancement request as well.
Cheers,
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Cameron
Online Community Manager/Moderator
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