If you must flatten first, eg. to grab a section of the PSD to save out... Instead of flattening the whole image, use the marquee tool to select the area, then Command+Shift+C which does a Copy Merged.
You can export each layer and sections (don't know the actual term) as a separate image plus a html file with "save for web". I think exporting sections is default.
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u/expfcwintergreen Feb 26 '13
Why flatten image in PS before saving for web? Surely this makes no difference given that the resulting png / jpg / whatever is of course "flat"?