Is it possible to refresh added columns on a worksheet when the columns
included in the query are refreshed?

For instance, I import items along with description, cost, vendor item
number, etc. Then next to that I will add columns calculating gross margin,
% of increase, etc. also for each item. If that item has been deleted, it
will be deleted after refresh, but the data I have added for that item in the
columns next to it still remain on my worksheet.

Is there a way I don't have to go in and manually change those columns not
in the query?

Most people have calculation set to Automatic, which means you have to
do nothing. Try F9 otherwise.