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Thank you for joining the thread, @keychain36.
Yes, deleting deposits with payments that are deposited under the Undeposited Funds will still become available to the on the Payments to Deposit window. if you wish to remove them from the lists, you may delete them manually. This may affect your invoices thus, I encourage checking your transactions carefully before doing the action.
On the other hand, the Undeposited Funds account is always available on the Chart of Accounts. If it's missing from there, the account may be renamed.
For additional reference about depositing payments into the Undeposited Funds account in QuickBooks Desktop, check out this article.
Post again if you have any other questions. I'm a few clicks away to help. Have a good day!