I have been experiencing an issue where the subtrees I have defined in SourceTree disappear after closing and restarting.
Since I had been having a lot of problems, I had been recreating the subtrees a fairly large number of times. Not sure if its related.
I eventually managed to fix this by deleting the contents of the subtree-cache in the .git folder.
I've attached the contents of the folder, not sure if its of any use. Hopefully it is.