Leave Without Pay On Disciplinary Grounds

I am working in Software Service based company.I have taken leave of 50 working days due to sickness.But my company doctor is not approving the certificates and medical documents I have submitted.
So my HR is asking me to write a letter stating that I was at fault and I have taken prolonged leave and will not repeat it in future.I have asked him about the consequence of this letter and he replied that as this is the first incident the company will issue me warning letter only.But I am not sure about it.Also I will mention that I am under a bond period of 2 year owing to an amount of 50000 .Please suggest
i)Are they going to take this letter and use it to ask for resignation?
ii)Will they mention it in my experience/relieving letter?
iii)What if I stick to my medical reasons and refuse to write the letter?

Hello Pareek,
What is/are the reason(s) for your Company Doctor to refuse the Approval?
I think more the details you give--of the sickness, the reason(s) for Approval refusal, your role/function in the company, etc--the better & practical the suggestions of the members.
However, prima facie, there's a strong element of 'probability' in your apprehensions--so better not take any hasty step.
All the Best.
Rgds,
TS

Hi, I have just completed one year in the company.I am a software developer in one of the projects of the company.I was suffering from typhoid
Please give suggestions whether to write letter or not?