What do you mean by “To call any plugin a third party plugin”? Custom Sidebars plugin is not part of our bundled plugins (see https://theme.co/apex/forum/t/troubleshooting-version-compatibility/195) and we cannot provide support for third party plugins or scripts due to the fact that there is simply no way to account for all of the potential variables at play when using another developer’s plugin or script. If a third party plugin played nicely or everything worked fine in the past, there’s no guarantee it will work in the future as we don’t have control over them.
In the previous screenshot I gave I see that they’re there in the admin Appearance > Sidebars. If you mean, there’s no selected post or pages then yes, I see no post or page enabled (checked) for your sidebars. This is what I want to investigate since you said it shows up in the front-end. But, I see your using another sidebar related third party plugin so that might be the one displaying the sidebar in the front-end.
If you’re afraid to test, copy your site to a staging server. This is a best development practice. Updating your site directly without testing is bad practice. We also have an article on that https://theme.co/apex/forum/t/setup-updating-your-themes-and-plugins/62. If you’re not sure how to do this, please hire a third party developer.
Regarding the question if your sidebars will come back, I’m not sure if they will come back since selecting a post or page in Appearance > Sidebars and using the Custom Sidebars plugin have the same function which is to display a specific sidebar in the front-end.
We need to check that other plugins are not affecting the features in X. Forgive me but this is necessary troubleshooting procedure. We can’t disable them for you as it is the site owner’s or user’s responsibility. We will help if there’s an issue with X and the bundled plugins. If there is a third party plugin conflict, we might provide a solution but note that we cannot guarantee an immediate fix.
Thank you for your understanding.