The basic strategy is simple: copy email files to a new folder that InfoClick can search, and then delete those emails from Apple Mail. The trick will be in carefully duplicating the files before deleting them. Continue reading for detailed instructions.
How to add emails to InfoClick and remove them from Apple Mail:
1. Create a new empty folder, which will serve as an email archive that you can add to InfoClick's search list. This folder can be anywhere on your Mac.
2. Open InfoClick's preferences. Under the "Email Folders" area, click the plus button to add the folder you established in step #1. To aid in the task of making absolutely sure you have properly archived all the desired emails (before you later delete them from Apple Mail) it would be best to remove all other folders from the list. That is, ensure that "Email Folders" only lists the new empty folder you just created.
3. Locate the desired email files on your hard drive. Apple Mail usually stores them in one (or both) of the following locations:
The .emlx files are usually organized by account, and then by subfolders that divide the emails by type and date. However, where exactly a particular email might be located can't be guaranteed, and the folders can be deep. An email sent through a gmail account might have a path like:
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InfoClick can help in this task. If you select an email in InfoClick's result listing and right-click it, the contextual menu command Reveal File in Finder will show you where Apple Mail is storing it.
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4. Once you've identified the email files you want to move out of Apple Mail, copy them to the new folder you established in step #1. You don't have to copy each email file one at a time; you can copy whole folders with any number of nested subfolders.
5. In InfoClick use the menu Database > Scan For New Emails. Once InfoClick has finished scanning for new emails, make sure the copied files are complete and the search results are as you expect.
6. You can now switch back to Apple Mail and delete the emails you copied, so they no longer appear in Mail.
WARNING: you should be absolutely sure all the desired emails have been duplicated before you delete them. If not, your emails may be permanently lost.
7. If you chose to remove all other email folders in step #2, you will need to add them back. Reopen InfoClick's preferences and click the plus button under "Email Folders" to add the standard folder(s) for Apple Mail, eg: ~/Library/Mail