How to put a folder in the git ignore, but she was tied to the project?

There are 2 options:
1. gitkeep
2. In the folder add .gitignore with the contents:

!.gitignore *

As I understand it, the problem arises from the fact that by default, when checking out code branch and just ignore untracked (untracked) files are not deleted from the working directory.

Preamble

You wrote that the new project files you have added in .gitignore. It's not a bad idea:

• It turns out that you have in the code of the old project is ignoring the new project files. In the branch the old code should not be that applies to the new.
  
• If you ignore a file new project, and then to remove them you need to either explicitly specify what files you want to remove or delete all ignored files. Among them may be such that you need, for example, the code of third-party delitek, if you have one, or your local configs, etc.
  

You can remove from .gitignore old project that relates to a new and just delete all untracked files and folders when checking out code using the command git clean-fd. But it is not very convenient because

• When switching between branches will be created and deleted many files, and this extra load on the FS time
  
• To enter these commands by hand most likely lazy (although you can write the alias for their automation)
  

The decision

Most likely in your case the most appropriate solution is to have two working directories for the current version of the project and for the new. And on the rare occasions when you get so that you make the switch between these two versions within the same working directory to run git clean-fd