Alterations to flat - procedure for regularisation

You took permission of the Society and then applied to BMC for permission. Had BMC given you permission? Have you got an acknowledged copy of your application to BMC giving sufficient details of the work you proposed to do?  Was there any reply from BMC?

You say "Now the society is claiming that I had made illegal alterations to my flat and the alterations were not as mentioned in the permission letter and have affected the building structure."

Is their claim partially or wholly right. There are three things (1) permission you sought (2) permission the Society gave and (3) what you actually carried out. Do all the three or at least (2) and (3) match without any half-trooths.  Only a competent authority can assess whether there is any structural damage. Has the Society explained what structural damage has been caused? Can you clearly assert what the Society says is not true.

No opinion can be given without knowing all the facts.