WHMCS and Paypal IPN integration error

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Hello, I am wondering if anyone has had this issue and what can be done to resolve it.
I have a customer with a monthly paypal payment and the IPN url set in paypal is different than the url that paypal is sending to. Apparently this is because after they signed up I moved the WHMCS installation to a subdomain ie. clients.mydomain.com. (I was advised to do this by Inmotion support).
Paypal is still trying to send the IPN to just mydomain.com. Paypal has told me I need to cancel the customer's account and get them to sign up again! (I am reluctant to do this as it doesn't look very professional).
The problem with this is that if I cancel their account their website will go down which is not an option as it is an ecommerce site and they will lose orders through no fault of their own.
Plus if they try and sign up again using the same domain name WHMCS won't let them as it is already being used in my WHM on the server.
Has anyone got any ideas on what I have to do to solve this? I can't get any support from WHMCS as it is licensed through Inmotion so I don't even have a WHMCS account to login for support.
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IMH Support Agent 5
Hellow cheesydoodles,

Thanks for submitting a question about WHMCS and Paypal. You mentioned moving the WHMCS installation to the subdomain. Though I'm not familiar with the reason Support provided for moving the installation, are you able to move it back or revert to a backup? That may give you some time to make alternate arrangements with Paypal. Perhaps Paypal support may be able to provide more information.

Best,
Christopher M.