"Reference does not exist" warning with \includeonly
This is a warning from the hyperref
package.
The hyperlinks you create to other chapters don't exist when using \includeonly
, but of course the reference itself is still valid.
You'll notice you don't get the warning when you compile the whole document together, because the hyperlinks do exist in this case.
Since you seem to be using \includeonly
only when you are working with just one chapter, you might not need any hyperref
generated links at that time. So consider the draft
package option.
Another clumsier possibility: write \renewcommand
s (or wrappers) for macros from the hyperref
package. Put them in your preamble right next to the \includeonly
and you'll remember to comment that stuff out all together when you compile the whole thesis.