here comes the ESRI fun, i have a published which has some invisible layers, at runtime im changing the definition query on different layers, everything works fine but i have noticed yesterday that when i zoom in, the features disappear, BUT not everywhere, in some two areas only.
im still investigating the problem, but still with no luck.
i'll updating on this issue.
UPDATE:
tried all the possibilities with no luck so what i though i would do is to create a new mxd with the same layers and it worked after that. so remember, when you find illogical reason solve it in the illogical way ;)