When deleting some parts (circled in red), the assembly seems to 'go bad.' I can no longer select a configuration. I can no longer save and get an error message (unknown error occurred wile accessing ...). I'll try to post the files next.
I'm not in front of my pc. But with a remote control software and my phone, I played a little with your file.
Your problem seems to be in the mirrored files. If you delete the mirror, then you can easily delete the parts you want without any error.
I'll check your file when I'm back to office, for a better answer. Hope since then it helps.
And personally, I prefer to use a design table or a configuration table for my configs. You don't have either of them in your main assembly.
I think I found the problem.
In your feature tree, select MirrorComponent1 and edit it.
Then click this arrow button
Next click each one of your components in above list and click this button. Until you have an opposite hand icon next to all.
ctrl+Q and save it.
Now if you delete each of those components everything will be fine.
I've attached a corrected assembly. Check if it works.
Retrieving data ...