You started wrong. You should have been invited to the app so you could download it from the teamserver.
It can be fixed but it is tricky. You should download the project from the teamserver and make sure that it is in a different directory. If other workers already made changes you need to do all your work again in this new project. If nobody else made changes you copy your .mpr from your old project directory to the one containing the teamserver version.
Do double check if everything is working when running locally and then you can commit your changes to the teamserver.
The most safe option is to rebuild everything in the teamserver version. And you can export microflows from your old project and import them in the teamserver version. Do note that if other persons changed that microflow also you loose their changes.
Thank you for your reply! I have been invited to the project after making the changes. Simply downloading the project and overriding it with the changed one will work or are there some possible complications?
make a new branch in Branch Line Manager, then select the team server app.