I have been doing some research on this phenomenon and will try to clarify: The good news is that everything remains in your account unless you empty your trash, and since there are no storage limits or concerns I recommend AGAINST emptying your gMail Trash. Here's why:
1) When you "Reply" to a message, your reply becomes part of a "conversation." You may have noticed that back-and-forth messages are displayed as one item with the replies "stacked" like notecards
2) If you "Label" a message (like moving it to a folder), any reply you make will stay in Sent Mail and any replies you receive will come to your Inbox. It is a good idea to label conversations that you may need to reference later rather than deleting them.
3) If you delete a message that is part of a conversation, the entire conversation moves to your Trash, including your Reply!
4) If you wish to save your reply in "Sent" but delete the original message, scroll up to the original message after you reply and click the down-arrow next to 'Reply," then choose "Delete This Message" instead of using the Delete button. Your reply will be in Sent Mail and the original will be in Trash.
For those of you looking for sent messages, look in (or search) your Trash!
When in doubt, clicking the down arrow next to "# more" (in the left column) will show you a label named "All Mail." Click on that to see EVERYTHING in your account, and search for what you are looking for.
Keep in mind that all email that goes in or out of our system is archived at the system level, so we can retrieve "critical" messages if you can't find them in your own account.