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If I understand the situation well, then the best and only(I think) way to go about this would be:
1. Take a package account(pkgacct) at the old host . This will include all your files and databases related to the addons as well.
2. Transfer it to the new server and restore it normally. This will create the main account and addons on the new server.
3. Now, using the cPanel, delete the addon domains ( Don't worry, the sub-directory and the files would still be there) .
4. Create individual accounts for the respective add-on domains on the new server.
5. Move the contents of the corresponding sub-directory to the respective accounts.
This might sound complicated but trust me it is simple enough!
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