As per discussion with Iulian Dragos the 30th July.
There are issues in refactoring when moving files to different packages which makes imports to the moved files wrong.

In my example I had a class Foo in a package com.company
which is referenced from file Bar.scala
then I moved it to a new package: com.company.baz
After, in my Bar.scala file the new import to com.company.baz.Foo did not replace the old, but replaced some random part of the file (the class declaration of Foo looked something like this:
class Fimport com.company.baz.Foo {)


I have tried to repro it using a simple test, but it was not reproducible on a simple system .
I was told to create a ticket either way so this is it. Since I am in the scala-ide office just come by I can try to show the issue in my actual code base.