Dan, a "soap and water" cleaner, i.e. alkalai, with good hot water rinses to
remove residual alkalai is the best non-solvent way to clean double treat
copper foil.  Unfortunately some of the discolorations you see will be
permanant and even if they won't functionally hurt you, may still be visible
after a good cleaning.

To be avoided are acids (which as you rightly point out will remove the
treatment, including any chromate anti-oxidant treatment) and mechanical
scrubs which will undo the reason for double-treat in the first place.

If the issue is cosmetics and can't be worked around by demonstrating
functionality, best to work closely with your suppliers and set up a
specification of some kind.  If you can agree on something then you've got a
solution.  If not, then maybe you're "tilting at windmills".

DT copper is easier to stain and discolor than shiny smooth copper and
probably will never look as "nice".  But it does provide good bond compared
to oxide and most people seem to consider that a good trade-off.

We sell lots of material with DT copper.  Have had no serious issues with
functional performance because of minor discolorations.

Chet Guiles
ARLON MED