Avoid overwriting your email files
I found your post because I needed to do the same thing. I succeeded! In my case, I have DSL on my network, and both computers can exchange files easily over the network. The emails I transferred were a total of more than 30MB, so they wouldn't fit onto a floppy.
You are absolutely right to be concerned about overwriting your emails. In OE, email "folders" are not subdirectories, but really just *.DBX files (while in contrast, the Store Folder actually is a subdirectory). So if you copy, say, your Inbox "folder" from one computer to the other, you will not merge Inbox messages, but rather the destination "folder" file Inbox.DBX will be overwritten with the source Inbox.DBX, and you will lose all your Inbox messages that were uniquely in the destination Inbox, but not the source Inbox.
After my suffering a lot of aggravation, I believe Import and Export do not function in the manner you need. Import works on entire subdirectories, not individual "folders" that are really *.DBX files, and Export goes off into fairyland.
Here's what worked for me. Read everything before you do anything, to make sure you understand, in case I didn't explain a particular step well enough.
First disconnect both computers from the internet, so you will not be downloading any new email from your ISP while you are doing the merge operation, and undo what you are trying to get done. I just unplugged the RJ45 to my modem.
I will refer to the computer you are going to abandon as the source, and the computer you are going to keep as the destination.
On the source, run OE and create a new folder (that is, a new *.DBX file) to hold the emails you wish to transfer to the destination. The new folder should have a unique name like "0" that does not conflict with any name of the existing "folders." [If you need to transfer emails from several OE "folders" on the source, you can create further "subfolders" beneath "0," also with nonconflicting (and readily identifiable) names such as 0inbox and 0sent, etc., to correspond to the current location of the emails you want to transfer, from within the Local Folders "folder."
Each "folder" and "subfolder" you create, results in a new *.DBX file, that is located in your Store Folder. Thus, the Store already contains an Inbox.DBX, and after you (maybe) create the 0inbox "folder," the Store will also then contain 0inbox.DBX. If you leave off the "0" prefix for the inbox folder you create, then OE starts numbering files, such as Inbox(1).DBX, and things start getting messier trying to figure out which number is the one you want, rather than just using nonconflicting "folder" names in the first place.
After you have created the "0" "folder" structure you want on the source, COPY the emails you want to move to the destination, to their appropriate location in the "0" "folders." DO NOT MOVE the emails - COPY them. NOTICE: if you left-click and drag an email, you will move it; that is you will copy it to the "0" place, and DELETE it from its current location. To copy the email, right-click and choose Copy to Folder..., and then navigate to the appropriate "0" "folder." After you have copied all the emails you want to transfer, close OE on the source.
On the destination, run OE and recreate the identical "0" "folder" structure that you created on the source. Close OE on the destination. Copy the 0*.DBX files from the source to the destination.
If you make a mistake, and instead copy the 0*.DBX files from the destination to the source, then the source "0" "folder" will be overwritten, and you will lose all the emails you put in there. And if you MOVED those emails instead of COPIED them, they are gone forever. Fortunately, you only copied the emails, instead of moved them, and so you just have to go back into OE on the source, copy the emails again to the "0" "folder," exit OE again, and then copy the 0".DBX files again.
When you reopen OE on the destination, it should now have within the "0" "folder" structure, all the emails you wanted to copy from the source. Now, it's just a matter of continuing on the destination within OE, and copying the emails from the "0" "folders" and "subfolders" back to their proper locations in the corresponding Local Folders. Finally, after you confirm all the emails are copied out of the "0" "folder(s)," you can delete the "0" "folder(s)." After you have deleted the "0" structure from within OE, the 0*.DBX files may still be lingering inside the Store Folder, so you may want to clean them up there as well.