I had this problem in the past, when my Internet was down and I worked offline, and most of my changes didn't appears in Team Explorer.
Following these steps:
First, In the solution explorer, select the folder that you want to re-conciliate (for me, it was my entire solution folder), and select Compare...
Click in Modify Filter, and in the filter text-box, you could type:
*.cs;!obj\;!bin\;!packages\;
In this example, it will include in the search only C# files and exclude in the folders: bin, obj and packages.
Notice the column Pending Change has the info whether the file is marked as edit, add, etc... or nothing...
- To mark as edit (when the local item has a matching server item), select the file and choose Check out for Edit...
- To mark as add (when the local item doesn't have any server item), select the file and choose Add Files
Finally, I am not sure why the projects are not listed here (after I remove *.cs filter, still doesn't show up), so rebuild the solution to make sure the projects updates as well
+ In the solution, click the connect button (if shows up) that said Go Online.