I think the concern stopping them from using the server now is the fear that the FBI modified "something" to log or report on traffic going through the server.
Absent the implementation questions of whether there will be anything useful in the logs, when someone takes you equipment and returns it later without comment, it is not unreasonable to assume that something happened to it.
(Note: I have participated in DoJ forensic training. The FBI procedures should be similar.)
As to the validity of the concern: Investigators are not usually allowed to mount storage media in read/write mode. If they do so, any evidence obtained from that media will no longer be admissible in court. While many labs do have non-forensic connectors for storage media, they are usually not used for fear of accidentally tampering with the evidence.
Investigators will make copies of media and manipulate the copies, but the originals will never be changed.
This does not say that there is no way from them to put some kind of logging software/firmware/hardware on the server, but it is pretty unlikely.