I'm using Sourcetree to mange a Bitbucket account for a Unity engine project I'm working on. Unity uses an Assets folder which holds image files, game world files, etc.
I created a branch to fix a bug, and inside this branch I deleted several files in the Assets folder (mostly PNG images) and added several new ones as well as modified some other pertinent files. I've commited the finished changes to that branch just fine, however now that I'm attempting to merge these changes into master, Sourcetree seems to act as if there are no changes to any of the files in this Assets folder. After it prompts me to resolve conflicts, when I look at the working copy the entire Assets directory isn't even visible when viewing "Pending" or "Conflicts" files. These files are visible when I select to view "Clean" files, and there seems to be no insinuation at all that the branch I'm attempting to merge from has deleted or added files in this directory.
Any ideas what's going on in this situation?
EDIT: The Assets directory is not specified in the .gitignore file.
EDIT2: If I use ctrl to select the master and branch together, I am able to view the changes which are correctly reflected. However the problem arises when attempting to merge.