To just make it work again (not using the --shell mode), you could handle reading your commands.txt
outside of inkscape and pass single commands to it. If you use xargs, you could run it even in parallel.
Assumming you have a commands.txt with all arguments in one line per input file, like
--export-filename=test72.png --export-width=72 input.svg
--export-filename=test36.png --export-width=36 input.svg
you could execute them as a batch like this:
cat commands.txt | xargs -P2 -L1 inkscape
-P<number>
optional: is the amount of threads you want to run in parallel (using not more than you have cpu cores in your device available is reasonable)
-L1
specifies how many non-empty lines of your input file are passed as arguments to inkscape