Answer supplied by David Teyssier:

The calibration uncertainties vary from one instrument to another. A summary of those is provided in each of the instrument overview pages, namely:

HIFI: https://www.cosmos.esa.int/web/herschel/hifi-overview

PACS: https://www.cosmos.esa.int/web/herschel/pacs-overview

SPIRE: https://www.cosmos.esa.int/web/herschel/spire-overview

The calibration uncertainties are provided in the Performance and Calibration section, typically with a distinction between absolute and relative (repeatability) accuracy. For HIFI a dedicated calibration uncertainty budget table exists per observation, and can be retrieved as an HPDP - see https://www.cosmos.esa.int/web/herschel/highly-processed-data-products.

The Herschel Science Centre has produced a number of short videotutorials about the analysis of data with the Herschel instruments. These contain information on the uncertainties in photometry and on the flux calibration of spectroscopy and how to treat the different effects that may influence it. You can find the videotutorials, which we recommend strongly viewing, here:

https://www.cosmos.esa.int/web/herschel/legacy-training-materials