You can pass extra parameters to the refmac run by placing the instructions into the file named "refmac-extra-params.txt". So just put "MAKE HOUT Y" there and see if the hydrogens are preserved.
> In my case Refmac run from inside coot does not preserve hydrogens if > present , such as the ones that prodrg puts in .., I will try using > modern refmac as Paul recommended... -- Coot verendus est
