The snapshot taken records two things:
1. What files you have on your computer
2. What registry items (and their data) you have on you computer.
When you install program "A" it will most likely put it's files in something like "C:\Program Files\A" and some registry-items in "HKLM\Software\A". This is what ZSoft Uninstaller will record. When you install program "B" it will put files and registry-items somewhere else, and therefor not interfere with program "A".
In short, it should be no problem what so ever to uninstall 'program 3 of 5'.
Naturally, if program "A" is a framework, or something like that, that is required for program "B" to work, when you uninstall program "A", program "B" will no longer work.
Putting all of another way: It will work as if you uninstalled it any other way, except that it might remove something that the regular uninstall-function wouldn't, but as was actually put on your computer by the installation program.
