If you are working from the source code you should never just get specific files, you always want all the updated files from the latest commit to the default branch. ie pull all changes in TortoiseHG Workbench, then close TortoiseHG Workbench and right click the top level folder and choose TortoiseHG > Update (make sure it says Default branch in the dialog). This updates your working copy with the latest files, then you need to rebuild the solution and generally you should also visit the /Setup/Default.aspx page in case any sql scripts have been added or updated.
If you are deploying an official release package then just download it again and replace the files in the /bin folder as I mentioned.