SonarLint for eclipse: Unnecessary changes to sqPrefixKey

We’re using SonarLint for Java (Version 4.0) in connected mode (SonarQube Server in Version 6.7.2) with Eclipse 4.10.
Because we have more than 1500 projects we’re analyzing we couldn’t bind every project manually in every developer’s IDE. The solution we came up with is to create a settings file for each project with serverId and projectKey already specified and pushing the settings file to source code management. This way, an individual developer only has to configure a server connection. This solution isn’t ideal, but it’s working flawlessly for those projects which are analyzed on the server.
However, for those projects currently not analyzed (mainly test projects; bound for when we enable analyzing our tests) the sqPrefixKey is modified whenever a configuration update is applied.

In the log file I get entries which seem fine:

Detected prefixes for projectA:
  IDE prefix: 
  Server side prefix: path/to/projects/projectA

However, there are multiple entries where server prefix is not correct:

Detected prefixes for projectB:
  IDE prefix: 
  Server side prefix: path/to/projects/projectZ
Detected prefixes for projectC:
  IDE prefix: 
  Server side prefix: path/to/projects/projectZ

This results in lots of changes which must be reverted (pushing the changes would not help, the next update might set projectY as sqPrefixKey).

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