Learn English – Is the construction “from then on … until now” correct/idiomatic

I would rather write the sentence as follows:

But now another problem might arise due to unknown unavailable edges, i.e. A-B and C-D, and should be avoided.

"And should be avoided" is referred to "another problem." You could also write the sentence as follows, but the sentence I wrote before would be understood too.

But now another problem might arise due to unknown unavailable edges, i.e. A-B and C-D, and it should be avoided.

Instead of introducing the parenthetical with commas, you can use parenthesis.

But now another problem might arise due to unknown unavailable edges (i.e. A-B and C-D) and it should be avoided.

"It's not as bad as all that"

This is a set phrase, an idiomatic formula of expression in which "all that" has no concrete meaning. "all that" just intensifies "not so bad". You might also say: Really, this is not so bad - or: This is really not so bad.

By the way, it is not so easy to find "not so/as adj as all that". I'm still trying to find it in Longman DCE. DCE has all determiner 1-17 and all adverb 1-18. In all adverb no.17 is "not all that" in similar uses but the use "not so/as adj as all that" is not registered there. I suppose it is in the entry "as".

I skimmed through two long entries of "as", found "not so aj/av as", but didn't find "not so/as adj as all that".

Of course, one could give "all that" some justification. One might say: It is not as bad as all that you have told me about the situation. All that is not so bad.