Comment # 19 on bug 1046277 from Dr. Werner Fink

(In reply to Aldo Bonfiglioli from comment #18)
> hp712:/usr/share/texmf/tex/generic/config/language.splits # ls -l
> /usr/share/texmf/tex/generic/config/language.splits/   
> total 468

[...]

> hp712:/usr/share/texmf/tex/generic/config/language.splits # ls -lt
> /etc/texmf/tex/generic/config/language.dat
> /etc/texmf/tex/generic/config/language.dat.lua
> /etc/texmf/tex/generic/config/language.def
> -rw-r--r-- 1 root root 17253 May 19 02:21
> /etc/texmf/tex/generic/config/language.dat.lua
> -rw-r--r-- 1 root root  7674 May 19 02:21
> /etc/texmf/tex/generic/config/language.def
> -rw-r--r-- 1 root root  6573 May 19 02:21
> /etc/texmf/tex/generic/config/language.dat
> 
> Those three seem to be out of date.....

Indeed ... try as root

   touch /var/run/texlive/run-hyphen
   /usr/share/texmf/texconfig/update

this should use the data in the splits directory and recreate the three main
hyhphen files.  After this the fmtutil-sys --refresh should do its work