I believe that this the same problem to the StreetPilot 2720. This lacked mass storage mode and was a right PITA. The fix in the link at the bottom of this page was confirmed as working with a Nav3 as mentioned by one of the people who posted on that thread.
If you're loading maps from Mapsource then your loading a gmapsupp.img file that contains all your mapping. This file format is intended as the supplementary mapping space on your GPS for extra mapping beyond the official region install that either came installed from the factory or was installed as an official mapping update. This primary mapping is in a file called gmapprom.img. Now this file can only be created by magical Garmin 'soup' within the update application. Your GPS will work without it but as you have no file access you can't delete it so it's there hogging the lions share of available space.
The gmapsupp.img and gmapprom.img files are the same format, only the file names are different. MapSource and MapInstall can only overwrite gmapsupp.img and the magical Garmin 'soup' can only overwrite gmapprom.img. Both files are overwritten by the respective upload/update processes. The two file names and the inaccessibility of the primary mapping is intentional on Garmin's part to preventing you accidentally over-writing the primary mapping.
Do you have some older mapping on there that's un-ticked in the Maps menu page? If so then that's your problem.
The easiest way to clear the majority of the space is, if you have an LM update subscription (I know these never were sold with this but you can buy them separately) is to do an update and load the region you want. You're never going to get all of Europe on there though.
Alternatively load the smallest region on offer, doesn't matter where as you won't be using it, which will reduce the size of the gmapprom.img file and thus free up room for any gmapsupp.img file you create in Mapsource and upload.
I did find a way many years ago to replace the US mapping on my import 2720 with a legitimately purchased copy of City Nav Europe. This converted the GPS from US to Euro spec. Some thing that Garmin told me was impossible. However, they still sold me the mapping (on DVD in those days) and the required unlock code. The expectation was that I would just use this alongside the installed US mapping that was hogging over half the internal memory (mapping was considerably smaller back the...). That wasn't good enough for me an being a persistent bugger I set about finding a way around this. I had far too much time in my hands then... I managed it and documented it whole thing on the SmellyBiker website forum which is now regrettably defunct (site still going buy forum was dumped). Luckily I grabbed the pages of the site before this happened and saved them locally. Will have a look at getting them onto one of my web servers over the next day or two and post a link back here. The procedure is not for the faint hearted though....
Carpe Diem... Updating primary mapping on Garmin StreetPilot and BMW Nav3 GPSs
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