Hi,
the cause for this is that the update needed to update an internal JavaScript library (for the features like sorting, searching, etc.). This updated library has some backward-compatibility breaks, and one of them is a modernized HTML/DOM structure (for example to make the table accessible for users with disabilities). This means that the CSS selectors also had to be changed, which now requires adjustments in the CSS code.
TablePress tries this itself during the update process, for all CSS code in the “Custom CSS” field on the “Plugin Options” screen. So, if your TablePress-specific styling is indeed in the theme’s style.css file, it could not be updated automatically.
But again, doing this manually is not a big problem. It would however be necessary that you update to TablePress 3.0 again, so that we can look at this.
If you don’t do this, you will have to stay on TablePress 2.4.4 forever, which I really don’t recommend.
Best wishes,
Tobias