We simply apply the changes to each file in turn. The existing replacement
logic is unchanged, except that it now no longer implicitly assumes we are
talking about the current buffer.
If a buffer is not visible for the requested file name, we open it in
a horizontal split, make the edits, then hide the window. Because this
can cause UI flickering, and leave hidden, modified buffers around, we
issue a warning to the user stating the number of files for which we are
going to do this. We pop up the quickfix list at the end of applying
the edits to allow the user to see what we changed.
If the user opts to abort due to, say, the file being open in another
window, we simply raise an error and give up, as undoing the changes
is too complex to do programatically, but trivial to do manually in such
a rare case.
Vim's QuickFix lists require 1-based columns, which is what is returned
from ycmd's commands.
As noted in the comments, the Vim documentation for setqflist is
somewhat vague about this "byte offset", but it is confirmed to mean
"1-based column number" both in testing and in :help getqflist.