They were fine before the FBI took them but not now?

They were never fine as deemed by the FBI.
The FBI however cannot claim use of the coins along with the original owner, owners, individuals, etc.
They must be wiped from the Bitcoin network since they are disputed within another network.
These outside network systems cannot create a negative impact on Bitcoin or it then defeats the purpose of using this system for holding and exchanging value on a global scale.
We the community are aware of these coins and they have been marked for this purpose, it does not matter how much you try to "wash" the coins, they will forever be locked in the Bitcoin system.