I suggest to implement the following three items to avoid this confusion:
- Add an extra option to disable any optimizations. There already exists a similar one "Settings→Formats→Write→JPEG→Optimize Huffman table", maybe add the same option in the same place, but name it "Optimize Huffman table during lossless transformations (reduces file size without any loss of quality)"
- Show an extra info message when you invoke the lossless transformation (which you can disable just like the warning about block sizes during the lossless crop), something like:
Lossless transformations can lead to a reduction in file size, but still without any loss in quality.
You can verify it by losslessly rotating an image 4 times, copying it, rotating it 4 more times and noting that it's identical to the first copy.
You can disable this in "Settings→Formats→Write→JPEG→Optimize Huffman table during lossless transformations", then even the first image rotated 4 times will be bit-for-bit identical to the original
- Retain the Progressive encoding type during lossless transform (so progressive images should not be converted to non-progressive)