I am currently using the following command to convert a PSD into a JPEG
convert.exe "input.psd" -flatten -resize 1280x-1 "output.jpg"
which outputs a JPEG that includes hidden layers.
Is there a way to flatten the PSD but ignore the hidden layers when creating the JPEG?
Try:
convert.exe "input.psd[0]" -resize 1280x-1 "output.jpg"
This just uses layer "1" which should be your completed psd file.
I do not know what the -1 in your resize is supposed to do.