When applying a patch file which contains multiple commits in one patch file, SourceTree gives some .rej rejection files, which is to be expected. The problem is that if for a single source file, there were rejections for diffs in multiple commits, only the latest rejected diff is contained in the .rej file.

This is in fact the git/hg default behaviour when applying a patch file which contains multiple commits in one patch file.

One way to resolve this is to not use combined multi-commit patch files. SourceTree has an option to create one patch per commit for this reason when creating patches.

However this can be a lot of tedious work, for instance with over 25 separate patch files.

A new feature suggestion for SourceTree would be to allows batch processing of patch files, i.e. one that allows to select multiple files which are then applied as patches subsequently. You could add an option that renames any .rej files created in each step to a unique name (maybe including the patch file name) to avoid the problem that .rej files get overwritten.