CRJ-900 pilot reported FMS failure inflight. The flight crew was able to use an ILS signal to divert to a nearby airport and land.

Narrative

Flight prior; the single FMS failed. Crew flew green needles into ZZZ1. Maintenance shutdown the airplane and replaced the FMS with a new one. Ground check was good but was still deferred per the MEL XX-XX-XX. During preflight for our flight; the FMS seemed to be working. The MEL did not prohibit the use of the FMS but prohibited the use of certain routes. We used the FMS to program the route. We tried to bring up the VORs in flight to have the airways setup if we needed them. About halfway to ZZZ2; our FMS failed; and we lost all navigation data. We were never able to receive a signal from any VOR along the route. We tried low and high enroute VORs but did not receive any VOR. The only signal we received was from the ILS in ZZZ2. We communicated with Dispatch about the malfunction and periodically asked about our position. We asked ATC if they can see us as a primary target or a secondary target. They saw our position based on the transponder's signal; so we knew that the airplane had an accurate GPS position; but we were unable to see it. Dispatch was also able to see it through their tracking software. As we continued; we did ask Dispatch about the plane. Specifically; I asked if they planned to have maintenance meet us at ZZZ2; swap airplanes; or cancel/delay the flight. We did not receive an answer and could not inquire as we prepared for arrival. In ZZZ2; we shut down the airplane for 10 minutes. During startup; the FMS was working again. We also performed a VOR receiver check using ZZZ2 VOT. The VOR passed the check. Our concern; as a crew; was that the airplane's navigation systems consistently passed checks on the ground and failed in flight. These failures happened twice in one day. The restart we accomplished never actually fixed any of the navigation systems. Without any reassurances that the airplane's navigation systems would not fail again; it did not make sense to accept the airplane. Another problem is that we were going to operate the flight at night into a congested airspace. This threat added more complexity to an already complex operation. We did not see a good chance for a safe outcome of the flight. In summary; without fixing the navigation issue; likely chance of losing all navigation data; flying at night; and flying in the airspace led to our decision to deny the airplane. FMS was deferred from previous flight. Maintenance involved a replacement of the FMS and a shutdown and restart of the airplane. No other work was done on the aircraft between the previous flight and our flight. Do more thorough work on maintenance than shutting off and restarting the airplane. Ground check was good; but failed to address underlying cause of the FMS failure. Operation recovery was poor. There was no proactive effort from the company to move a replacement aircraft into position; have maintenance ready for us; or delay/cancel a flight. The flight crew communicated multiple times our needs and suggestions for operations with no plan from the company.