Upgrade from AX 2012 FP (CU3) to AX 2012 R3 (CU9) creates duplicate legal entities

Hi,

I upgraded AX 2012 FP (CU3)  to AX 2012 R3 (CU9) system and it created 2 duplicate entities of what were already there.

I had Default DAT company and my customized company, say 'ABC' .

Upgrade to R3 created duplicate of these legal entities keeping 'DataArea' column as blank for both of them.

This creates issue in synchronization as 'DataArea' field is part of an unique Index on the table CompanyInfo.  

Another different thing I noticed is that 'PartyNumber' field for these 2 new (duplicate) entities contains some GUID value. I am not sure where it came from.

Anyone faced these before and know the reason of it and what is the impact if I delete these duplicate records?