I have tuned organs at various pitches as best suited for the organ.
First check the wind pressure to verify that it is appropriate for the
type of organ you are working on, and compatible with and appropriate
for the cutup of the flue pipe mouths.
Pick a few flue pipes which are in good condition for trial tuning.
Good condition means windways are crisp with little damage, upper
lips are undamaged with little warpage, and tuning slides and tuning
stoppers are leaktight. Tune these pipes to where they are "happy".
Happy is nice timbre, similar "apparent" volume, and with tuning slides
approximately set at the half way point, and the tops of tuning
stoppers inserted 1/4 to 1/2 the pipe width into the pipe.
The pitch that these pipes are playing is a good indicator of what the
organ pitch should be. It is important to start off close to original
tuned pitch for an organ, because the reeds will only produce the most
pleasing timbre within a small range of pitch. Changing the pitch of
reeds while retaining proper timbre can be done, but only by someone
who does this sort of work.