On the current upstream:
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$ licenserecon
fi: Versions: licenserecon '16.0' licensecheck '3.3.9-1'
Parsing Source Tree ....
Reading d/copyright ....
Running licensecheck ....
No significant differences found
-----
On the upcoming upstream:
-----
$ licenserecon
fi: Versions: licenserecon '16.0' licensecheck '3.3.9-1'
Parsing Source Tree ....
Reading d/copyright ....
** Superfluous file pattern configure
** Superfluous file pattern ltmain.sh
** Superfluous file pattern m4/libtool.m4
** Superfluous file pattern src/ntpctl.8
Running licensecheck ....
d/copyright | licensecheck
FSFULLR | FSFAP m4/ax_add_fortify_source.m4
FSFULLR | FSFAP m4/ax_check_compile_flag.m4
FSFULLR | ISC m4/check-libc-compat.m4
FSFULLR | ISC m4/check-os-options.m4
FSFULLR | ISC m4/disable-compiler-warnings.m4
-----
Those are all files whose license changes according to which variant (BSD, GNU, etc.) of autoconf/libtool/m4, etc. upstream used to produce a new release. As such, IMHO, there is zero point in updating d/copyright at every release just to match changes in license for such auto-generated files, let alone to report any discrepancy as an error. They should therefore be ignored by licensereconf and licensecheck.
Martin-Éric