When I put Levitation level 3 on myself I'm unable to override it with /effect giving myself Levitation level 254.
What it should do is instead of propelling me up, start lowering me down to the ground.
Instead it extends the duration of the existing effect.
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Sorry, I didn't word myself properly. Edited now. I do know it's /effect <selector> <id> <time> <lvl>

please provide exact commands used

/effect @p levitation 9999 10 true
/effect @p levitation 9999 250 true
Tested on singleplayer.

you're using value's that aren't supported

Yes they are because they work for me if I use them alone.
More over I know for a fact that the same situation with a different status effect in 1.8.7 works and properly overrides it.

try it with level 1,2,3 and 4, at least then you can see the number of the amplifier of the effect

What you suggested works, but it doesn't fix the issue. This worked for levels as big as 250 in 1.8.7 so it is a bug.

yet those values aren't supported
if it works for lower levels, it works for higher lavels
Invalid
it's /effect player effect duarion level
invalid