All reports of debhelper-tools-from-autotools-dev-are-deprecated for the archive. The extended description of this tag is:
The debhelper tools from autotools-dev has been replaced by the tool dh_update_autotools_config, which was available in debhelper (>= 9.20160114)
The dh_update_autotools_config is run by default via the dh command sequencer. If you are using dh, you can probably just remove the uses of the tooling from autotools-dev without doing any further changes.
If you use the "classic" debhelper style, then please replace all calls to dh_autotools-dev_updateconfig with dh_update_autotools_config. The calls to dh_autotools-dev_restoreconfig are replaced by dh_clean, so they can most likely just be removed without any further changes.
Refer to https://bugs.debian.org/878528 for details.
This tag has not been emitted in any package tested by Lintian.