One is Item Memory. If you have any Item Memory-affecting sprite or object in the same vertical line within the same screen, then collecting it and going off screen then coming back will cause the flower to disappear. The most common culprit for this is regular coins, but it could also be red coins, winged clouds, and a variety of other sprites.
If your level has 4 sublevels or fewer, ensure that each has a different Item Memory index. If it has 5 or more then that's not possible, and if two sublevels share the same Item Memory index then items in one sublevel will affect Item Memory in the other, so you basically need to resort to trial and error to determine which item caused it to disappear.
The other likely cause is Super FX sprite limits. Basically, when there are several Super FX sprites on screen (generally, these are sprites that rotate or stretch in some way, such as Piranha Plants) new Super FX sprites might not spawn. The 0FA flower uses Super FX (the 110 flower does not, but it might not be usable in your sprite set) so try removing some Super FX sprites that are nearby.