TL 2019 - inconsistent processing of environment variable TEXINPUTS

[Pablo González L]

> When I set TEXINPUTS as a windows environment variable in the OS
> settings, everything works as expected.

If it works for you configuring "windows environment variable", it's better
to leave it that way. If it is tedious to do it in graphical mode you can do
it from cmd: (without admin "C:\Users\yourname>"):
Open a and run:
$ setx TEXINPUTS .;D:/path/goes/here//;
Close it and open a new one (without admin "C:\Users\yourname>") and run
$ kpsewhich -var-value=TEXINPUTS
This configuration is global and you don't have to write it over and over again.
If you want to see the system variables
$ reg query HKEY_CURRENT_USER\Environment
And if you want to delete it (to add a new one for example)
$ reg delete HKEY_CURRENT_USER\Environment /v TEXINPUTS /f

> But when I try to set it via the appropriate config-file
> ${basedir}/2019/texmf.cnf, TL messes up my whole PATH setting and
> terminates with ?! LaTeX Error: File `my/file.tex' not found.?
>

If you insist on doing this using a configuration file you can do this. You open
a cmd console (without admin "C:\Users\yourname>") and run:
$ kpsewhich -all texmf.cnf
By default the TeXLive installation does not set this variable, you should get
something like this:
c:/texlive/2019/texmf.cnf
c:/texlive/2019/texmf-dist/web2c/texmf.cnf
Now you run:
$ setx TEXMFCNF C:/Users/yourname;
Close it and open a new one (without admin "C:\Users\yourname>") and run
$ echo TEXINPUTS.xetex=.;D:/path/goes/here//; > texmf.cnf

> The TL documentation recommends to make all changes to the defaults in
> ${basedir}/2019/texmf.cnf:
That's true, but if you execute:
$ tlmgr conf --help
you will notice that the "TEXINPUTS" option is no longer available with a clear
warning message at the end:
        Warning: The general facility for changing configuration values is
        here, but tinkering with settings in this way is strongly
        discouraged. Again, no error checking on either keys or values is
        done, so any sort of breakage is possible.

I think the documentation is unclear on this point. These settings are local
and will only affect your system user account, if you use admin permissions
they will be for everyone, so you avoid modifying:
c:/texlive/2019/texmf.cnf
c:/texlive/2019/texmf-dist/web2c/texmf.cnf

Saludos