Could please someone help me get on track and see why the files aren't indexed correctly? They disappear from the sinkhole folder but do not show up in the search sources. In the splunkd.log I don't see any errors related to the file.
I managed to find a solution to this problem, the configuration is correct only the problem was that the user running the splunkd service on the windows machine was a local user and not a domain user. Switching to domain user solved the problem.
However, I'm now faced with another problem - what to do when the files are collected from a different network domain which splunk does not have access to?