Loss of accented characters

We have a good number of pdfs distilled from Quark 4.1, which I think uses (in our case) Acrobat Distiller 3.01.

I edited one using Acrobat Professional 8.1.0, replacing two pages with pages from another pdf, also coming from Quark.

Acrobat Professional 8.1.0 threw away the accented small caps in the edited pdf, replacing them with spaces... since our work is in French, this matters more than a little.

Is this a known problem? Do I need to ensure (if I can!) that the original fonts are accessible during an edit operation? What else should I look out for?

I also have a problem with these pdfs given that the figures 0 through 9 were not in the usual position in the font. I think they were usually in a separate font reserved for non-lining figures. They display ok, but are not found in searches. Is there a remedy here?

Cordially,

Andrew Brown, in France near Geneva