If a paper is accepted but not included in the conference proceedings, does organization (IEEE) retain the copyright of the paper? In case a paper is accepted but not included in the conference proceedings (conference fee not paid), does the organization (IEEE) retains the copyright of the paper?

Consider the case that none of the authors is able to attend the conference to present the paper and possibly they would like to submit it to another conference in the near future. 

We have only uploaded the paper to PDF eXpress and then to the online platform of the conference. The copyright transfer will be signed at the end of the conference following verification of attendance.
Restating your conditions,


Copyright form not signed
Conference fee not paid
Paper not in proceedings


This implies that your paper is not published in this conference. Hence by no means can IEEE hold copyright for your manuscript with regard to this conference.

For a conference that requires fees, the respective paper it's published when the sum is paid (although there are exceptions). IEEE conferences seldom require you to sign the copyright form before the payment. They are usually done together. Once, I've noticed that some participants signed the copyright form on the day of the conference since they missed out on attaching the form along with the fee (which was successfully paid).