Hi,
We've also been encountering this problem under similar circumstances - TFS 2017 Update 2, TFVC, SonarQube v6.7 (and earlier), using the SonarQube build extension for TFS (currently v4.1.1). We have a number of build agents in the same queue, spread across multiple build servers, and the builds are set to clean sources as well. All our solutions are built for Visual Studio 2017 (MSBuild 15).
It looks to me as though on some builds some or all of the projects in the solution are just not getting their files analysed, so the analysis process updates SonarQube as though those files no longer exist and closes all the issues on those files. A subsequent run then recreates the issues, but obviously they don't have any of the manual changes we might have made ("Won't Fix", etc.). Looking at the issues in SonarQube it's possible to see all the closed issues with their history, so for us it's not just that the same issues are losing their status; they are being closed and new issues created as though it's a new file. I don't know if this is the same for other people who have encountered this?
It's not always all the projects in the solution, and it's not happening all the time. The Activity graph from the project pages shows where it has happened (all of these dips are where some or all of the issues have been lost, rather than developer changes, and sometimes it affects more files than others):

Comparing the analysis logs from two different runs, the only difference in the output where a project lost all its issues is that there is an extra line in the log for that project: "2018-03-29T09:01:33.2400332Z INFO: 0/0 source files have been analyzed." There were the same number of files indexed each time and nothing else to indicate why they weren't analysed.
Is there any way we could get more detailed information from the analysis that might provide more detail as to why the files weren't analysed?
Thanks,
Andrew