Was the softener bypassed during this time, or was there a regular supply of water flowing through it?
I re-activated a "stagnant" softener about 4 years ago immediately started failing well water tests due to coliform bacteria. Eventually I figured out it was the softener and not the well. It has since been replaced.
That one had been bypassed for who knows how long, which is worse than keeping water running through the beads and simply not adding salt.
For the brine tank (pictured in your post) let the salt run out on purpose and bring it outside and rinse it out once a year.
Brine water is very sterile. Stuff can't grow in it.
$16 cad @ home depot