There is basically nothing that can make a properly created income account “disappear” except you manually deleting it. And Manager will not let you delete an account when any transaction has referenced it. You can rename an account, even an automatically created control account, but you cannot delete one that has been used.
I conclude from this fact that your transactions were never posted to a properly created income account. However, some of your comments make it difficulty to tell exactly what you have been talking about, because you have switched back and forth from deposits to invoices to income to payments. All those terms mean different things.
Another possibility I can think of is that you renamed and possibly recategorized the former control account Customer credits. Quite a while ago, this automatic account was deprecated as part of restructuring the function of Accounts receivable. Transactions with customers that might have correctly been posted to that account in older versions of Manager were transferred to Accounts receivable without user action. If you were doing something strange that involved this (possibly renamed) account, the affected transactions could have somehow ended up in Suspense upon your update when incorrect prior records could not be correctly interpreted.
Every time you share a little more about your procedures, possibilities point more strongly toward the likelihood that you were not correctly posting transactions in your old version. You have said some things that point toward incorrect use of Accounts receivable, others that might involve Customer credits, and still others that involve sales invoices and receipts. All of those are tightly coupled. And your use of cash basis accounting could have been hiding the errors. (That’s one reason accountants prefer accrual basis accounting.)
You’ve already done a test proving the new version works properly. I think your best course of action is to stop looking for a magical fix and correct your old transactions.