Hi @Alex29,
based on the investigation the following TICKET was created and tackled, fixing this bug that only happened on Windows and when the output/build directory was set to be the project base directory.
The fix is currently available on the SonarLint for Eclipse Dogfooding Update Site and will be released with 10.9 planned towards early November.
@alef75 just fyi, this sadly won’t fix your issue and I will continue the investigation and the discussion in the other Thread.
Thanks both of you for your feedback, all the information you provided and the help you provided with testing build artifacts on your side! 
Best,
Tobias