I use Visual Studio with GIT/Assembla and in most projects when I change a file there is a red check mark before the file in the Solution Explorer, meaning it can be commited later via GIT/Assembla.
However, in one project, there are files and after saving changes from a file in that project, a red check flag is shown, but is automatically removed after a few seconds. Also when I try to commit the changes to the local/remote repository, that changed file is not in the list (thus it will never be part of the remote repository).
I removed (manually) a .git folder inside the project where the files are are, so it looks like a sort of git-sub project inside the solution.
Does anybody know how to fix this problem?
The .git folder is your local git repository - this folder contains information about the remote as well as the history, tags, branches and other information for your git repository. Removing this is probably what caused your issues.
I would create a new project, clone the git repo from Assembla again, then copy your changes over from your old project.