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: