In team work, if someone add new source file but not use visualgdb, after update with upstream, those new file will be found by visualgdb and push to remote linux but vs project not updated automatically.
That is by design, as VisualGDB cannot distinguish between source files added by someone else and generated files or temporary files.
Note that this should not stop VisualGDB from building and debugging the project correctly if the Makefile was updated by the person adding a new source file.
There are many ways in which the source files can be listed in a Makefile and no possible way to support all of them.
Are you using VisualGDB-generated makefiles or your own makefile layout?