Removing Mail folders from "On My Mac" section Apple Mail 5.3 0n 10.7.5

Hello,
I typically move read mail out of my Inbox to various folders I have created on the "On My Mac" section of the side in Apple Mail 5.3 running on 10.7.5.
I have folders like these dating back to 2009!!!
I recently decided that after archiving the messages as PDFs, I could reduce my Library > Mail folder size.
I deleted 5 folders total.  They no longer appear in the "On My Mac" section even after restarting the computer.
I happened to take a look at my Users/xxx/Library/Mail folder and noticed that three of the five folders I deleted are still listed in the Mail folder but now report a size of 0 bytes.  (If it makes a difference, my folders in the On My Mac section are nested but only two layers deep at most)
Did I make an error at some point when deleting the mailboxes that resulted in three of them still appearing in the Mail folder as 0 bytes???
Is it safe to manually delete the three .mbox files in the Mail folder that no longer appear in the sidebar and report a size of 0 bytes??
Thanks
John

Hey Kappy,
I don't think I communicated this properly in my original post.
The 5 mailboxes I deleted from the "On My Mac" section of the sidebar where in fact deleted by Ctrl-clicking each one and selecting Delete.
After closing Mail, I took a look in the Mail folder an found that 2 of the 5 were in fact totally gone but the remaining three are still listed but now empty.
I then opened and closed Mail a couple of times and restarted my computer once and they were still present.
After you last message, I moved the 3 empty .mbox files out of the Mail folder to a temp location and since then after several times opening and closing Mail and 2 computer restarts they have NOT returned and Mail seem to continue to function and all of the other mailboxes in the On My Mac section are still present and populated.
I was just curious why after deleting 5 mailboxes, only two were completely removed and the other three were only emptied.
Thanks for you assistance by the way . . .
John

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