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I wrote this problem to IDM. Top support - by the way. Problem could be reproduced and is logged in the internal tracking system. Probably solved with one of the next updates.

Hi there. I'm new to UEStudio - mine is version 15.10.0.11. I created a project with a local dir (and files) and a ftp connection to the projects server. There are no problems to upload the whole project directory in 'project manager' -> 'project' -> right click on 'project dir' -> 'upload to server...