If a few have been replaced - check that it was with consent.
Yes they do look out of place in my opinion, in most windows, in historic buildings. And you rarely get an exact copy and lose the historic glass. Far better to repair what's there if possible.
The size of the average window in a period building rarely means vast heat loss. Most loss is through draughts - but you need some ventilation.
Have a look at Storm Windows for quite neat secondray glazing, if it really is an issue.
