will my sub domains be working if i delete the main domain? If not, is there a way to transfer 100+ files to a new sub domain quick and easily?

Your domains (or sub-domains) are only “mapped” to certain directories (or sub-directories) in your account. So the easiest way to kind of “move” them is to map your new sub-domain to the original directory and/or to rename it for better organizational purpose.

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