Priority register for transfer

If you are not satisfied with their oral reply you may make a representation in writing to the competent authority directly through proper channel venting out your grievances and seek his intervention and relief to your problems. 

Whether priority can be deleted if resignation not accepted as per rule

Since you have already tendered resignation and if the rule states that upon resignation the seniority will come down, then the law will prevail.

But resignation is not accepted. 

That period is considered as leave without pay

It is but natural that the period of absence or leave without salary may be considered as dies non hence the promotion senioryt list would be amended accordingly deducting the period of dies non from the quealfying service for the ensuing promotion

First of all please clarify whether you have taken any legal action on the issue, if not what prevented you from initiating legal action because it affects your future career. 

You are entitled to certain rights as per law and the regulations, which cannot be left to be decided to the whims of some crooked people sitting as officer over you. 

You can consult a prudent and experienced service law practising advocate and take his opinion in person on all such further issues