Did you open the model the second time again through home.mendix.com > project > Edit in Studio Pro?
In that case, you might have downloaded a second copy of the model from the team server.
My advice is to open a model where you already are working on through Studio Pro directly.
In your case I would check out the folder where you do have stored the Mendix models. You will probably see 2 folders for the same project. Where one is name {ProjectName}_2. Delete this one. Open the correct folder without _2 and open the model
In the future;
If you are in doubt you have the right branch, click choose branch line. Here you can also check if there is already a local copy.
I had gone through same path Mendix Home page>My apps > Edit in studio pro and then refleted to Mendix Studio pro app for edtiting.