I tried to fill in an area to replace powered_comparator (non-subtraction mode) with powered_comparator (subtraction mode) using the command:

/fill x1 y1 z1 x2 y2 z2 minecraft:powered_comparator 4 replace minecraft:powered_comparator

But, I got the error message: Data tag phrasing failed: Invalid tag encountered, expected "{" as first char. So, I tried this command:

/fill x1 y1 z1 x2 y2 z2 minecraft:powered_comparator 4 replace {id:"minecraft:powered_comparator"}

That didn't give me an error message, but it did just fill the entire area instead of replacing the comparators.
This command works, though:

/fill x1 y1 z1 x2 y2 z2 minecraft:powered_comparator 4 replace [block not a comparator]