"I do not want to delete a transaction, I want to remove the reminder from the Enter Memorized Transaction prompt when the company file is opened."

Yes, I understand this. I use the functions for 84 entries every month, and about 3 dozen at year end.

"The actual Memorized Transaction List that I can edit after startup has already been modified to reschedule the transactions, but these old prompts continue to appear."

Then perhaps something is corrupt in your file. Edit the transactions to confirm their settings because that is the Only place this is controlled. You set it for Remind Me, or Automatic (nearly all of mine are Automatic, which means it asks my  Permission), or Do Not Remind Me.

Confirm the setting, in the list, and/or edit them to examine them.

"I want to delete the prompt, not a nonexistent transaction."

Yes, I understand this.

Have you tried File menu > Utilities, Rebuild this file?

Then, Delete the entry in the List will remove the Instructions entirely. Or;

Edit the entry in the List = change its behavior.