Hi recently we have an application issue which requires patching of sun solaris.
Problem is that there are many zones created in this solaris server which are used by other applications.
So if it is possible that certain patches could affect the current applications.
What is the best way to handle this kind of situation?
The solution really depends entirely on where the problem lies and what sort of fix you're applying. In many cases, if the problem is in the kernel, you can patch it in such a way that the patch will only apply to a process with a given flag. If it's in a library or some such, you could have a harder time. In short, we really need a lot more info to give you a solid answer.
If you're patching the kernel, then your patches affect everyone: there's only one copy of the kernel.
If you're patching application software, then you can apply those patches to affect only certain zones.
Have a look at the Zones FAQ.
Is the patch you need to apply timezone-related? If not, you may be able to only apply the one patch.
Your best bet is to set up a staging system that's software-wise identical to this box, get it working, and then install your patches and test.