This sounds like you have created a route in Flitestar which has varying levels within it. If you then generate an ICAO flight plan from that, it will have the level (or speed) changes within the route.
This is acceptable as an
IFR (Eurocontrol) flight plan; indeed, it can be essential to do that in order to get the route accepted because different airways are open at different levels.
If however you are flying
VFR, nobody cares what (plausible) level you put on the flight plan. VFR flight plans are not checked for any validity - except in some places like Montenegro or Albania where somebody might actually look at it and chuck it out of they don't like it.
Are you saying that if you copy/paste such a multi-level route into ais.org.uk it doesn't like it? That would be pretty bad. Still, for notam purposes, it doesn't usually matter. The narrow route briefing works ok if done at one single low level (say 2000ft) for the whole route; one just ignores the warnings of low flying kites
Or are you using some built-in notam feature in Flitestar? I have never used anything like that.
The vertical airspace depiction feature of FS is nice but I find it of limited use. There is so much restricted airspace in France that picking one's way through it is very hard. One needs to get the SIA 1:1M charts; these come with a handbook which lists every one of the areas and the levels and opening times. A lot of them are closed at weekends, for example. An even better way to fly in France is to follow the airway routes; typically at FL065 and above. French ATC really like them. They avoid the restricted bits.