Commercial Fixed Wing
Flight Crew Air Transport Pilot (ATP)
Confusion
Deviation - Altitude Overshoot; Deviation - Altitude Crossing Restriction Not Met; Deviation / Discrepancy - Procedural Clearance
Air Traffic Control Issued New Clearance; Air Traffic Control Provided Assistance; Flight Crew Requested ATC Assistance / Clarification
Procedure; Human Factors
I was the FO flying the ZZZZZY arrival at ZZZZZ intersection. The proper arrival was put into the FMS and all waypoints were checked for accuracy. As a new descent speed was input to the FMC; the plane increased descent to accelerate to that speed and did not level at FL240 at ZZZZZ intersection as desired on the VNAV profile. By the time I noticed and corrected; we had descended about 1;200 feet too low. Somehow; the crossing altitude at ZZZZZ had dropped out of the FMS. The Captain immediately called ATC and informed them and they indicated no worries just go direct ZZZZZ1. Remainder of arrival and landing was uneventful.This was my first flight leg as pilot flying in about 3 months and the end of a long trip; so my crosscheck may not have been as sharp as I would have preferred. I'm not sure when or why the altitude at ZZZZZ was dropped from the FMC unless I inadvertently pushed the altitude selector knob when entering the 6;000 foot final altitude on the arrival into the altitude window. I will have to be more careful in the future about setting and double checking all altitudes at each waypoint during departure and arrival and making any needed corrections in a more timely manner.
As I came back from break; the FO and Relief Pilot said that they had the correct arrival in the FMS and that they checked the points. I also went through all the points; speeds and altitudes; which were correct. As we approached ZZZZZ intersection; the speed started to come back prematurely. The FO entered 290 and the three of us verified all was correct prior to executing. The aircraft started to pitch down. We noticed right away it wasn't stopping at FL240. The FO who was flying immediately started to correct. Not sure just how low we got. I quickly checked the legs page and sure enough; the crossing had dropped out. I immediately notified ATC who was not concerned and cleared us to ZZZZZ1 intersection for the uneventful remainder of the arrival and landing.Even though we were ending a long flight we did not feel fatigued and the three of us were following all the procedures. Not sure what caused the altitude restriction to drop out by simply updating the descent speed. As I stated above; we caught it; but not before it went below FL240. Even though we haven't flown much recently; we all felt comfortable and we were day VFR and not rushed.I am struggling to determine what we could have done differently. As I stated above; we were not rushed and were following all the FMS procedures. The only thing that was changed; was the speed. There was no re-sequencing of waypoints that could have caused the restriction to drop off.
Air carrier flight crew reported a waypoint crossing altitude dropping out of the FMS and not knowing why resulting in an altitude deviation.