It is certainly not broken, I recently copied a project over from one DN to another via C6 just recently and it worked like expected.
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Make sure your Digitone is set to send and receive over USB only in the MIDI Port Config menu. This ensures maximum data transfer speed when connected via USB.
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Open C6 and configure it to send and receive with the connected Digitone in the Configure window, and check so that there is no delay set under the misc section.
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Load whichever Project you want to send from the Digitone and navigate to the SysEx Send/Receive menu. Hit Receive in C6, then select ‘Whole Project’ under the Send option in the SysEx menu.
Press Stop in C6 when the Digitone has finished transferring.
The data received should be around 2.9MB in size.
Now, make sure to select the received data and save it as a .syx
(If you just hit save without selecting any file in the C6 window list you will save a file list instead. These end in .c6)
Sending a Project to a Digitone (and any other unit) can be done at any time, you just need to connect to your unit in C6 and hit send. The whole project data will be sent in, and anything that is currently in RAM that is occupying the same space will be overwritten by the incoming data.