I have seen this many times especially Europe to Asia. If you 'make space' by deleting the waypoints at the end of the flight it can change the final fuel calculations if it's not a straight line, so to speak. I always looked for waypoints way down-route on the same track and deleted them. You have to high-light on the plan in some way to avoid not loading them back in. I used a red pen. Normally once the SID is completed and established in initial CRZ there is plenty of room to re-enter the deleted waypoints and fix it all up.
I also, always made sure that my partner in crime was aware of what was deleted and he also marked his copy of the plan. If the deleted waypoints are on the same track in a straight line you are at least protected and the FMC predictions are accurate.
It all sounds very suspect but by constantly cross checking and recording any deletions on the flight plan I never had any problems. The box needs more memory and it's a weakness of the system.