Yes I've noticed this too.
You could try disabling all options in print.prt and instead request "object hydrograph" outputs using the "object.prt" file. This will generate daily outputs for a specific spatial object - eg only one HRU or channel instead of all of them.
This is described in the latest SWAT+ outputs document, though I'm not sure all of its features are enabled yet. Here is an example (for gis_id 1):
object.prt: written by rswat on 2021-04-28 01:09:46
NUMB OBTYP OBTYPNO HYDTYP FILENAME
1 sdc 1 tot ohg_sdc_1_tot.ohg
The filename "object.prt" must be added to file.cio to activate this output. It seems to be a much faster way of getting discharge values.
I'm still not sure of the meaning of all of the output columns it produces (they are missing the usual units header lines), so I would be interested to hear if anyone else has successfully used
object hydrographs in their project.
Dean