1."It is not always necessary,however, we use it to link two parts of that instrument".

‘However’ can be used to join two simple sentences to make a compound sentence.

But in (1) there is a mistake while using the punctuation "however", and the comma after "necesssary".

This is corrected by using semicolon and comma like this

"It is always not necessary; however, we use it to link two parts of that instrument".

This is OK to me, and I have no doubt here.

2."It is always not necessary, however, when we use it to link two parts of that instrument".

I think there are two mistakes here. The first is, using comma before necessary and the other is after conjuctive adverb a subordinate clause is used.

Here is my question. Can we use a subordinate conjunction after the conjunctive adverb?