I'm sorry to hear you've found yourself in this situation. I understand this may be a frustrating issue to resolve as I'm not aware of any automated solution for dealing with it.
To clarify, for those who don't know the details, Go Daddy may require a user rearrange files if there are more than 1024 files in any single folder. That's a lot of files to be in one place, and having more than that negatively affects performance of the hosting servers. This rule is in place to protect performance for other users who share the server(s).
Thankfully, most users do not encounter this problem because the default setting for WordPress is to organize uploaded files by year and month. With that enabled, you'd only have an issue if you generated more than 1024 files in the uploads area in a single calendar month.
As for updating your existing site, you can update individual posts by editing the path in the HTML of individual posts, but as I said earlier, I'm not aware of how this can be automated or done in bulk.
In response to Nihad, you should NOT get an additional violation notice once the issue is resolved. We want our customers to be happy and successful. We do need to have some rules in place to keep things running smoothly for all users, but I like to think we're fair and accommodating when issues like this arise.
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