Upgrading package does not generate new subscription token.

[captainolive]

I'm having trouble figuring out how to troubleshoot this issue. 
 
In short, I have one client who downgraded a package (from 9.99 to 5.99) and paid the invoice in PayPal, then paid the new invoice the following month in PayPal, yet the 1st official payment of the monthly invoice after the upgrade did not set up a recurring payment token in my PayPal for 5.99.   
 
I noticed the past due invoice for 5.99, and both myself and the client expected this to happen since it was the first true invoice of the new hosting package, and I had the opportunity to see first hand, with my own eyes, the clients process from signing on, paying the invoice with paypal, and we did not see any options on the paypal merchant portal to configure a subscription. After making the payment, I received confirmation of the funds, as well as the invoice is paid, but there were no new subscriptions listed in my recurring payments log on paypal for the customer or the 5.99 amount.
 
At this rate, it appears the client will have to manually pay each invoice, and I don't know what else I can do to troubleshoot. 

It’s possible I caused this issue by canceling the old subscription token in paypal itself. When the client first downgraded last month to 5.99, and I received confirmation of payment, that customers active subscription profile DID NOT change prices or cancel itself, even after paying the invoice upon downgrading. There was still an active subscription for 9.99. In fear that the client would get billed under table by a rogue active paypal subscription separately, AND receive a 2nd invoice for the new package 5.99 package, I manually cancel the 9.99 paypal subscription via paypal, and set the expectation that the next bill would have to be manually paid to trigger/begin that recurring token, but unfortunately that was not the case. 
 
I’m concerned because there were no issues with prior 9.99 service, and no issues with new customers who started on the 5.99 either, and the client did a clean upgrade in the client upgrade area. Everything worked flawlessly aside from changing affecting the paypal subscription. Considering the client already waited a full month manually and begin the new subscription, what else is left for me to test or try for this to work? 
 
Luckily no one else has upgraded or downgraded on my service, but without understanding this better, I’m worried at the thought of what would happen if everyone were to decide to upgrade/downgrade at once.
 
I’m slowly getting concerned because it's the same issue for DOMAINS. Luckily no one notices the inconvenience because it is once a year, but for some reason, domains DO NOT setup tokens even when customers select auto renew from the beginning. I can set up my own auto-renewal in enom, but it appears as if my WHMCS will not setup yearly subscription tokens for domains, OR transitions to new upgrades or downgrades.

If anyone here has their WHMCS auto charging domain invoices and upgraded packages without manual intervention please let me know if you had the same issue and how you resolve it, because as of right now everything works automatically and perfectly so long as they dont want to upgrade or change anything later on 😕 

Thanks!