There are two 'types' to be aware of with a quickfix window:

1. entry: the actual line content (e.g. :grep foo will show a specific line that matched within a file).
2. file: the actual file itself (e.g. the path to the file that contained the match).

If you want to replace content in a file you need to choose whether you want to apply the change via the quickfix 'entry' or via the 'file' as a whole.

This is best demonstrated by examples...

To execute a substitution for every 'entry' listed in the quickfix window use cdo:

:cdo s/v2/v3 | update

To execute a macro for every 'file' listed in the quickfix window use cfdo:

:cfdo execute "norm @q" | update