Ive been using tortoiseMerge as external tool in source tree for a while now but today I had 3 conflicts after pull, so I fixed the first one then I wanna open the next and window pops up saying Visual merge in progress, but nothing happens, tortoise is not launching.
How could that happen?
It works one second and than it doesn't...
I did some search but did not really find much, I tried to change diff tool in source tree from system default to tortoise, but that did nothing.
Any ideas what happened?

This can happen if one of the files is deleted.
You can run the following command in a command prompt in windows, to be able to answer the question git-mergetool asks when one of the files (or even both) is deleted.
Use your own CONFLICTED_FILE_PATH, and you may need to use a different path to point to your git-mergetool: