I've discovered the "fix" but also wanted to note the issue. It may have been fixed in newer versions but in a version I downloaded in February 2021 of this tool I was unaware I needed to create a new folder to export the BIDS data to and instead attempted to download it to an existing folder. This resulted in the deletion of said folder and a series of errors. Not realizing the folder had been deleted and suspecting the errors were due to the proximity of the folder to the data I tried again, this time using the desktop as the destination - this wiped my desktop. The files on the desktop have not been recoverable even with help from my IT department. The fix is simply to have an empty folder as the destination and everything works fine. However, losing my other files clearly was not ideal (thankfully most were backed up).
I've discovered the "fix" but also wanted to note the issue. It may have been fixed in newer versions but in a version I downloaded in February 2021 of this tool I was unaware I needed to create a new folder to export the BIDS data to and instead attempted to download it to an existing folder. This resulted in the deletion of said folder and a series of errors. Not realizing the folder had been deleted and suspecting the errors were due to the proximity of the folder to the data I tried again, this time using the desktop as the destination - this wiped my desktop. The files on the desktop have not been recoverable even with help from my IT department. The fix is simply to have an empty folder as the destination and everything works fine. However, losing my other files clearly was not ideal (thankfully most were backed up).