Date: 202010
Local time of day: 1201-1800
Location: ZZZ.ARTCC, US
Aircraft: Medium Transport
Operator: Corporate
Operating under: Part 91
Flight plan: IFR
Mission: Personal
Flight phase: Cruise
Airspace: Class A ZZZ
ATC / advisory: Center ZZZ
Reporter organization: Corporate
Reporter function: Captain
Reporter qualification: Flight Crew Instrument; Flight Crew Multiengine; Flight Crew Flight Instructor; Flight Crew Air Transport Pilot (ATP)
Human factors: Situational Awareness; Communication Breakdown; Confusion
Anomaly: ATC Issue All Types; Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy
Detector: Person Flight Crew
When detected: In-flight
Result: General None Reported / Taken
Contributing factors: Staffing; Environment - Non Weather Related; Human Factors
Primary problem: Ambiguous

Narrative: This event was a complex setup with numerous contributing factors that led to a slight and uneventful course deviation on a flight from ZZZ to ZZZ1. Having spent 30+ years in the part of the US I was quite familiar with the dynamics of the environment. In preparing the flight; I ran a prelim flight plan which recommended a route I would expect; a SID that meshed with the ZZZZZ3 arrival to ZZZ1. For arrivals from the south into ZZZ1 it is customary and without exception have flown the ZZZZZ3 which runs with the arrivals and departures to several airports. There were numerous TFR's along and around the route of flight this day. I filed a flight plan using app which recommended a different route; a SID to Victor airways; no STAR into ZZZ1. It was presumed this route was preferred to accommodate the numerous TFR's. I know for certain in the app I had selected FL230 as I wanted to either be rerouted as necessary for the TFRs or be above as the TFRs were below FL180. These issues were disclosed; briefed between the two pilots prior to filing flight plan; discussed verbally in the takeoff briefing; and even added extra fuel for possible reroute. When our clearance was obtained to depart ZZZ; it was for the SID and Victor airways as filed with app; further reinforcing the presumption that it was ATC preferred due to the TFR's. The final altitude cleared was 17;000 feet due to the Victor airways chosen; not FL230 as was desired.As we began our taxi; we were expecting Runway XX for departure which was a fairly long taxi. Traffic was light; and Ground Control stated Runway XXC was available which we accepted. This now being a very short taxi. I stated to the copilot would taxi slowly to allow time to load new departure runway in FMS; the SID chart was retrieved; compared to the FMS; and the takeoff briefing verbally amended accordingly. In doing these things; we verified only page one of the flight plan in the FMS. At this point we were not aware that in reloading the departure RW; the FMS had on the second page not only inserted a discontinuity; but had deleted two waypoints; the last one on the SID and first point on the filed Victor airway.As we were flying the departure and level at 15;000 feet; we crossed the second to last waypoint on the SID. At this point when the FMS sequenced; the discontinuity appeared on page one. This FMS has known issues and several Service Information Letters (SIL's) from the manufacturer regarding runway changes with SIDs and STARs. Having seen the occurrence a vast number of times for arrivals when changing or loading the arrival runway after the STAR; the resolve had always been to delete the discontinuity as no waypoints had ever been seen deleted and verify altitude/speed restrictions. When the discontinuity appeared on page one of the FMS flight plan; it was simply deleted without verifying the fix meshed with the filed route. As two waypoints had also been deleted; this created the issue at hand. Soon after we crossed the waypoint in question; ATC asked if we were beginning our RH turn. This exchange revealed the error at hand and we were given a vector. Believe it was just prior to that waypoint that ATC asked if we could join the ZZZZZ3 arrival; to which we stated yes. The Controller stated this will be vectors to join the ZZZZZ3 and cleared us to 17;000 feet. At this point we inserted the missing waypoints and queried ATC to confirm our currently assigned route. ATC again stated expect the ZZZZZ3 without confirming assigned route; and did not provide an expect to waypoint to join the ZZZZZ3. A level of uncertainty remained as the ZZZZZ3 has six (6) transitions into the arrival. We briefed and had STAR displayed to deal with the coming short notice for the join waypoint as the fixes along this arrival are close together with several altitude and speed restrictions. Throughout this event; we could hear ATC transmitting to other aircraft; but never heard other aircraft respond; thus the controller was obviously working multiple frequencies/sectors with a resulting high workload likely contributing to not providing and expect to waypoint. This also presented a certain level of distraction on our part. Once we were cleared to a waypoint on the ZZZZZ3; and with a descend via clearance; the remainder of the flight was uneventful. The slight deviation actually took us further away from the TFRs; no restricted airspace was encroached; and there were no traffic conflicts.




Synopsis: Corporate Captain reported a track heading deviation during departure and cited ATC workload as a contributing factor.