Maybe tex 'knows' nothing about some of your fonts. So before recreating all formats, you have to run kpsewhich in a shell. (for an exhaustive explanation about kpathsea and kpsewhich: )
Kpathsea reads runtime configuration files named texmf.cnf for search path and other definitions. The search path used to look for these configuration files is named TEXMFCNF.
Kpathsea reads all texmf.cnf files in the search path, not just the first one found; definitions in earlier files override those in later files. Thus, if the search path is ‘.:$TEXMF’, values from ./texmf.cnf override those from $TEXMF/texmf.cnf.
If Kpathsea cannot find any texmf.cnf file, it reports a warning including all the directories it checked.
Kpsewhich is a path lookup and expansion for kpathsea. See manpage. man kpsewhich
Updmap or updmap-sys updates the default font map files used by pdftex, dvips, and dvipdfm(x), and optionally pxdvi, as determined by all configuration files updmap.cfg (the ones returned by running "kpsewhich --all updmap.cfg").
Among other things, these map files are used to determine which fonts should be used as bitmaps and which as outlines, and to determine which font files are included in the PDF or PostScript output.
Updmap-sys is intended to affect the system-wide configuration, while updmap affects personal configuration files only, overriding the system files. As a consequence, once updmap has been run, even a single time, running updmap-sys no longer has any effect (updmap-sys issues a warning in this situation). By default, the TeX filename database (ls-R) is also updated.
The command mktexlsr is used to generate the ls-R databases used by the kpathsea
library. It will create them for the specified directories, or for a default list if no directories are specified.
So the right order to add fonts or files to tex is
put the added files on the right location
control configuration files of kapthsea via kpsewhich
updmap-sys or updmap
mktexlsr
regenerating formats