"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 \renewcommands (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.