When Importing Mail From Apple Mail, you may find that the number of messages shown in EagleFiler is not the same as the number show in Mail. Although it’s understandable that this could cause concern, it’s usually not an indication that anything went wrong. Here are some reasons the counts could differ:
EagleFiler may show fewer messages than Mail because EagleFiler automatically skips messages that are exact duplicates. This is described more in the Handling Duplicate Messages in Apple Mail section of the manual. You can see whether this has happened because it’s reported in the mailbox’s note.
EagleFiler may show more messages than Mail because Mail sometimes hides messages that are approximate duplicates (e.g. the same message received twice in different accounts), but EagleFiler doesn’t skip them because they’re not exact duplicates. In order to investigate this, you can set Mail to show duplicate messages by entering this command in Terminal:
defaults write com.apple.mail _AlwaysShowDuplicates -bool true
and restarting Mail. You may need to first give the Terminal app Full Disk Access in System Settings ‣ Privacy Security.
Another possibility depends on how you imported. If you select specific messages and press the capture key, EagleFiler finds those particular messages and imports them. If you select just a mailbox and press the capture key, it reads all the messages in that folder on disk. Sometimes Mail’s disk storage gets out of sync with its database, so there may be messages still there that Mail thinks it has moved or deleted. These could show up as “extras” in EagleFiler if you import in this way.
It’s also possible, though unlikely, that something in the message data is confusing EagleFiler such that it wrote the right number of messages to disk but didn’t read them back properly. You could test that theory by importing the EagleFiler mailbox file into another mail app and checking how many messages that app finds.