Select All, then Remove Selected tries to delete current file
TLDR: In PrusaConnect, the select all check box selects the file currently being printed, even though that file doesn't have a check box.
In Prusa Connect while a print is in progress, select the printer, select the "Printer Files" tab, click on the select all checkbox that hovers above the check boxes for each individual file. Then select "Remove Selected" and "Confirm". You will get a message saying either that a read only file cannot be deleted or "File cannot be deleted as it is being printed". I believe this is because the file in progress is being selected under the covers even though there is no checkbox and no visual indication that it is selected.
You can work around this by refreshing the page and individually selecting the files, then clicking on "Remove Selected".