I really doubt giving them the vitamins during the treatment would lessen the treatment. The Treatment stops the protozoa from using B1. Medicated feed has extra B1 in it and it works in most cases.
They really should get B1 ASAP, so I would give them B1 during the 1/2 dose second treatment.
If you do not give them the second 5 to 7 day treatment, they will likely be sick again it 2 or 3 weeks.
Corid(amprolium)works by blocking thiamine from the body. Parasite needs thiamine(B1)to reproduce,by blocking the thiamine and starving the parasite reproduction stops and parasite is under control,allowing the body to build immunity to the specific strain it was. If you give vitamins during treatment,you are counteracting the medication. Medicated feed does not have enough Amprolium in it to help with an overload/outbreak,therefore the vitamins added to medicated feed are not an issue.
I have always argued with people that the Corid inhibits the thiamine in the coccidia it self, not in the body. Here is one website that describes the action of the drug: http://caribbean.merial.com/livestock/Products/Pages/corid.aspxWhat about feed that has B1 in it? Should we look for a different feed when treating them?