Kindly check appointment letter, bond, and any other document on which you have affixed your signatures towards your acceptance and see if it mentioned that period mentioned in bond/service agreement signed by you shall not include notice period.
Apparently, if there is no explicit expression, in bond that notice period shall not be covered in bond period, and then notice period should be counted in period of bond.
You have posted that: "But company is asking to serve notice period after completion of bond". Who has made this statement? Has the company stated so in writing or verbally? Usually such statements are made verbally. Employee should record all such transactions (audio/visual), and arrange some witness.
You may submit a gentle acknowledgment in writing by letter under acknowledgment addressed to company personnel who have signed on bond, good offices of your appointing authority, MD, CEO, Company Secretary with a copy to Head-HR, expressing that in the document titled as............(bond) dated...........there is no explicit statement that notice period shall not be counted in period of ...........years, for which you should serve the company. However on dated..........Mr/Ms..........designation.....dept.........address........has stated verbally in person to you that notice period shall not be counted in period of bond. Good offices should clarify the reason in writing for imposition of extra .........2 months on you.
If you have already served the notice of resignation, you may mention it. You should mention the effective date of resignation/last day in office in your notice. If you have not mentioned it you may supply a subsequent communication under acknowledgment, and may add that notice period with effective date of resignation/last day in office is counted in bond period and company may acknowledge the receipt in writing and issue instructions to you in writing by letter thru redg. post.
Yu may avoid sending emails from official email id of the company which can be blocked anytime by the company. Or you should forward the email to your personal email id. Preferably you may communicate by letter thru redg. post. You may keep copy of all documents/emails which can be useful to you.
In the employment applications usually new employer asks to mention court case etc. You may not conceal or misrepresent. However you should your new employer into confidence and if questions are raised you may clarify. The opposite party can approach new employer with vindictive approach. You must not reveal your employment/enterprise.
Try to be in employment where you shall have demand, role and you are indispensable.