Hi Fernando, In my opinion, the word "whether" cannot be used in your case. Moreover, it seems your sentence is incomplete; i.e. " {this is a cause} … If the company's use of assets and process of running the operation are effective or not, ... {sentence is missing - what a result should be} ...". Anyway, "whether" might be used inside the sentence; e.g. "If the company's use of assets and process of running the operation are whether effective, it will be discarded".

You are correct. It should be whether when accompanied by "or not". However, it is not uncommon to hear "if ... or not". But "whether" is more correct.

It would help if you provided the rest of the paragraph so we can see the full context in which "if" was used.

To answer this, we need more context as the words before and after the sentence will determine which should be used.