MySQL asumirá la parte antes de que el igual haga referencia a las columnas nombradas en la cláusula INSERT INTO, y la segunda parte hará referencia a las columnas SELECT.
INSERT INTO lee(exp_id, created_by, location, animal, starttime, endtime, entct,
inact, inadur, inadist,
smlct, smldur, smldist,
larct, lardur, lardist,
emptyct, emptydur)
SELECT id, uid, t.location, t.animal, t.starttime, t.endtime, t.entct,
t.inact, t.inadur, t.inadist,
t.smlct, t.smldur, t.smldist,
t.larct, t.lardur, t.lardist,
t.emptyct, t.emptydur
FROM tmp t WHERE uid=x
ON DUPLICATE KEY UPDATE entct=t.entct, inact=t.inact, ...
