This is usually not normal JPEG color loss. Based on the answers, the bigger issue is how Photoshop flattens layers when masks and certain blending modes are involved.

A likely cause is that a mask on a lower layer is affecting layers above it during merge/flatten/export. Photoshop may preserve that mask behavior when flattening, which can make colors or edits seem to disappear. If you merge only selected layers, Photoshop may warn you and offer to apply the mask first—but that warning does not always appear when exporting or flattening the whole document.

Another factor is that fine details can render differently when multiple layers use different blending modes; this can change the final appearance and may be image-dependent.

What to try:

• Check masks on underlying layers; one may be masking the edits above it.
• Apply or disable suspect masks before flattening/exporting.
• Merge smaller groups step by step and compare results.
• If blending modes are involved, test simplifying them or converting parts of the edit before final export.

So the problem is more likely layer-mask/blending behavior during flattening than simply working in the wrong color space.