In your case the facts and record point out that although you have resigned and trained the replacement Employee Company is quoting its internal policies and imposing a decision to declare you absconding. The emails in your file shall help you.
Represent to the good offices by a letter/notice (which you can also send) and describe the facts and conclude that you are being unnecessarily harassed and bad reference check in future is being flaunted at you and this is creating terror/fear in your mind as this step of the company is aimed at rendering your education/experience worthless and you shall not be able to earn your livelihood. Request the good offices to correct the wrongdoing of its subordinate offices and supply you the acceptance of resignation, work experience/service certificate, relieving letter with good comments in line with your performance, settlement of your FNF a/c and disbursement of payment and assurance that no bad reference/BG check shall be caused by the company against you. You may mention that you are expecting a relief from good offices in writing to be supplied to you say within next 7 days by redg. post before you seek legal advice and approach lawful authority for reddressal of your grievances.
If the good offices do not grant any relief then you may approach a competent and experienced service lawyer, o/o Labor Commissioner, wages inspector.