We are seriously considering moving URO to Counterparty after out 6 month distribution phase.
Some of our community members have expressed concerns that Bitcoin Core may be modified to prevent Counterparty from working in future versions down the track.
Is this a genuine concern of just FUD?
Also, can anyone link me to a few academic papers reviewing the security of Counterparty against counterfeiting of tokens of faking transactions?
That is FUD. There are many ways to store Counterparty data in the blockchain. It's not leaving any time soon, no worries. Everything is stored in the blockchain, and cannot be changed or manipulated without manipulating the blockchain itself.
Regarding the security, you can look at any academic papers that show the security of the Bitcoin blockchain. Also, the Counterparty source code has been reviewed by well respected Bitcoin security experts Sergio Lerner and Peter Todd.