Mail is unable to find responses to emails and missing messages

Since making the change to apple mail about 90 days ago, I have had an ongoing problem with missing messages sent from my desktop and iphone. They are not in the sent folder or the separate project email folder. However, the arrow next to the original message shows that the original email was responded to. When I click on the arrow, I receive a message saying that it cannot find the message and that I may have deleted the message.
I moved the Mail folder from the Caches folder and still no help.
I am required to keep all email messages sent and received. But this is an ongoing problem that has resulted in several lost messages. If I cannot resolve this issue, I may need to switch to a different email program.

oops sorry, Mailbox Behaviors: Drafts, store messages on server is checked. Notes, Store notes in inbox is checked. Sent, Store sent messages on server is checked and it is set to never delete sent messages. Junk, nothing is checked and delete junk messages when: is set to never. Trash, move deleted messages to the trash mailbox is checked along with, Store deleted messages on the server. Permanently erase deleted messages when, is set on, One week old.
i also use a mac laptop from time to time but the missing messages were sent from the desktop.

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