This is an issue for anyone currently developing on windows. i.e. when making (e.g. after a git checkout), make will reconfigure but for the linux environment, rather than the windows environment (even if this was what has only been done so far).
A fix would be to store the configuration of the relevant variables that influence the ./configure so that these are re-used each time.
This is due to CONFIG_SITE (specific to the windows build notes):
CONFIG_SITE=$PWD/depends/x86_64-w64-mingw32/share/config.site ./configure --prefix=/
An alternative way to provide the config.site that is remembered would be welcome, not sure this exists at all.
(FWIW you can also do ./configure --prefix=$PWD/depends/x86_64-w64-mingw32, I think that survives reconfigures, however then you can't usefully install the result with make install)
How about adding to the build document an instruction to add CONFIG_SITE as an environment variable to the .bashrc file?
Could do that, though I'd personally be wary of adding bitcoin build specific arguments to my .bashrc file. It might also cause conflicts: CONFIG_SITE is used by all programs that are configured using autotools.