Generally, they stick at least from a major W3 TC release to the next.
Every time you want to upgrade (including minors) you should back up the configuration first. Then upgrade, see if you get your site royally broken (I mean, beyond just losing some visual effects. I mean errors 500 and that kind of bad) then you downgrade and wait for 1-2 W3 TC minors, i.e. 9.3.1 - 9.3.2 and then try again.
Also, since you went the "manual minification way", every time you install a plug in you should check the minification wizard shown in my tutorial. It's quite frequent for new installed plug ins to come with their own CSS and Javascript, those are to be added to the existing minification list for a better website YSlow and SEO optimization.
On the other side, upgrading certain plug ins like NextGen you may get W3 TC warnings about it being unable to find certain files.
You'll see red warnings at the top of the WP admin window about this.
In this case, the plug in authors moved / renamed / removed certain javascript / CSS from their newest release yet W3 TC is still instructed to minify those files.
You'll have to go to W3 TC minify list and manually remove the files it complains the lack of.