Here's an actual example of the problem:
diffoscope --exclude-command stat /gnu/store/igc79crx5ya5vwyzkd2l95nlpbk647in-texlive-union-49435{,-check}
--- /gnu/store/igc79crx5ya5vwyzkd2l95nlpbk647in-texlive-union-49435
+++ /gnu/store/igc79crx5ya5vwyzkd2l95nlpbk647in-texlive-union-49435-check
??? share
? ??? texmf-var
? ? ??? web2c
? ? ? ??? updmap.log
? ? ? ? @@ -1,9 +1,9 @@
? ? ? ? updmap version r44331 (2017-05-14 02:15:43 +0000)
? ? ? ? -Wed Sep 11 01:17:36 2019
? ? ? ? +Wed Sep 11 01:17:33 2019
? ? ? ?
? ? ? ? Using the following config files:
? ? ? ?
? ? ? ? updmap is creating new map files
? ? ? ? using the following configuration:
? ? ? ? LW35 font names : URWkb (default)
? ? ? ? prefer outlines : true (default)
? ? ? ? @@ -795,26 +795,26 @@
? ? ? ? tmro108r
? ? ? ? tmui108r
? ? ? ? zd
? ? ? ? zpzdr-reversed
? ? ? ?
? ? ? ? Files generated:
? ? ? ? /gnu/store/igc79crx5ya5vwyzkd2l95nlpbk647in-texlive-union-49435/share/texmf-var/fonts/map/dvips/updmap:
? ? ? ? - 15888 2019-09-11 01:17:36 builtin35.map
? ? ? ? - 21361 2019-09-11 01:17:36 download35.map
? ? ? ? - 21361 2019-09-11 01:17:36 psfonts_pk.map
? ? ? ? - 21361 2019-09-11 01:17:36 psfonts_t1.map
? ? ? ? - 21356 2019-09-11 01:17:36 ps2pk.map
? ? ? ? - 14 2019-09-11 01:17:36 psfonts.map -> psfonts_t1.map
? ? ? ? + 15888 2019-09-11 01:17:33 builtin35.map
? ? ? ? + 21361 2019-09-11 01:17:33 download35.map
? ? ? ? + 21361 2019-09-11 01:17:33 psfonts_pk.map
? ? ? ? + 21361 2019-09-11 01:17:33 psfonts_t1.map
? ? ? ? + 21356 2019-09-11 01:17:33 ps2pk.map
? ? ? ? + 14 2019-09-11 01:17:33 psfonts.map -> psfonts_t1.map
? ? ? ? /gnu/store/igc79crx5ya5vwyzkd2l95nlpbk647in-texlive-union-49435/share/texmf-var/fonts/map/pdftex/updmap:
? ? ? ? - 21363 2019-09-11 01:17:36 pdftex_dl14.map
? ? ? ? - 19698 2019-09-11 01:17:36 pdftex_ndl14.map
? ? ? ? - 15 2019-09-11 01:17:36 pdftex.map -> pdftex_dl14.map
? ? ? ? + 21363 2019-09-11 01:17:33 pdftex_dl14.map
? ? ? ? + 19698 2019-09-11 01:17:33 pdftex_ndl14.map
? ? ? ? + 15 2019-09-11 01:17:33 pdftex.map -> pdftex_dl14.map
? ? ? ? /gnu/store/igc79crx5ya5vwyzkd2l95nlpbk647in-texlive-union-49435/share/texmf-var/fonts/map/dvipdfmx/updmap:
? ? ? ? - 411 2019-09-11 01:17:36 kanjix.map
? ? ? ? + 411 2019-09-11 01:17:33 kanjix.map
? ? ? ?
? ? ? ? WARNING: updmap has found mismatched files!
? ? ? ?
? ? ? ? The following files have been generated as listed above,
? ? ? ? but will not be found because overriding files exist, listed below.
? ? ? ? builtin35.map:
? ? ? ? download35.map: