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This issue seems to arise when "git qfold ..." is invoked from within a subdirectory of the working tree; the content of the specified patch(es) is not merged into the target patch, but the unmerged patches are deleted anyway, (unless the "--keep" option is in effect), thus resulting in destruction of patch content.
This is an insidious fault, because the failure to merge the patch content is not detected, and the loss of content goes undiagnosed.
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This is yet another CWD issue. The patches record file paths relative to the top level directory of the git work tree, which must be the current working directory, when any patch is applied; git qfold was not meeting this requirement, if invoked from within any other working directory.
Commit #1da2daa3 addresses the requirement for setting CWD, when git qfold is run. The insidious failure to diagnose any problem, when CWD is incorrect, appears to be a failing of git itself; specifically, when git apply is run with the wrong CWD, it does nothing useful — the patch is not applied, there is no diagnostic output, and no usable exit code. Yuck!
The correction of CWD, which is as far as I will pursue this issue, will be incorporated into the next package release.