Even though some of the primer remained, it was still affected by the chemical stripper. Any time that you use a chemical stripper, you have to remove every single layer and every trace of paint, primer and filler. ANYTHING touched by stripper that remains will cause adhesion problems when you re-coat it.
We scrape, then scrub with soapy water and a scotch-brite pad. Rinse, completely dry, then blast or sand any remaining material off.