When someone is picked up by the FBI, they leave the county system and enter federal custody, which means they will no longer appear in the county jail's records. That explains why the facility is telling you he is not there even though the same location keeps coming up in searches. He has been moved and the databases have not caught up or are simply not showing his new location.
Here is how to track him down.
Search the federal BOP inmate locator. Go to bop.gov and use the inmate locator tool to search by name. If he has been formally processed into a Bureau of Prisons facility, he will appear there. Be aware that it can take several days to a week after transfer before someone shows up in the federal system.
Check whether he is being held in a county jail on federal behalf. The FBI sometimes holds people in local or county jails under federal detainer while cases are being processed. If that is the case, he may not appear in the BOP system at all. In this situation, calling the US Marshals Service for the district where he was arrested is the most direct path. The Marshals manage prisoner transport and housing for the federal court system and can often locate someone who does not yet appear in public databases.
Contact the federal public defender's office. If your father has or will have a federal public defender, that office can locate him once he is in the system and can communicate with him on legal matters.
Contact the FBI field office directly. The field office that made the arrest may be able to confirm custody status, though they are not obligated to share details of an ongoing investigation.
Three weeks without contact after an FBI pickup is not unusual during the initial processing period. Once he is placed in a facility and his account is set up, contact should resume.
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