First myself not from Karnatak , myself from Maharashtra (So accept my limitation in State Law of Karnatak , But Some acts of central is also affecting your transcation and most state law are almost same with little varion so wants to give try , may not be 100% correct but 60-70%)
1. In Maharashtra Under one District , there are various sub registrar and you can register with any sub registrar . So if same thing has happened in your case , so it is ok. For this query you have to visit Registration office of District or that Sub registrar office , try to talk or get information form Govt. employee or officer in
2. Since the document is registered 1 or 2 year back myself sure , your state too have scaned the document and kept in it. Get Certified Scan copy of all documents. For getting certified scan copy you need registration no. date , registrar office (where it was done). Purpose of this is you will get correct document which is registered there.
3. Whether Original Builder is availble , I feel it is only 1 or 2 year newly constructed building ,Try to meet him and get Rectification Deed done , Register it at same place between him and the original person. With this all content will be made straight (Well this is what is safest method)
4. Once This two documents that original deed , rectrificaton deed is done then you can move with your transaction of purchasing that flat and you make proper sale deed mentioning Details of orignal deed and also mentioning what is in rectificatin deed what are rectification done and presumed now. Rectification Deed is required to be registered at same Place.
5. Additionally you requre Good local Advocate who knows about property law to check remaining all documents whether they are in order, Whether Land records, Society , Municipal records, Building Plan sanction is there or not whether title is proper or not. So you take help of some good advocate from your city and get it done. For Rectification Deed , you will need advocate he will do it . Registation fee etc. for it , any addiional nominal stamp duty will be calculated by him and he can put things in order
6. I feel althought not that much imp. still better you do rectification deed of original sale deed because in future you people don't come or world is small so they too are not available so , once remaining it remains forever and after 10-15 years next person to have same problem some time. Property transcation try to do as legal as you can , it is for life time single investment for most