> Is there is chance that micro controller will give some bad result because earlier
> i programmed .bin file in wrong way?
Unlikely. The programming erases all of the Flash and then burns the new code in.
But you should check any logs that the programming creates, and any options that it gives you to make sure that is happening.
It might be possible that it can be set up to only erase the part of the Flash that you are loading new code into. So there might be "stale pages" with old data in it. That shouldn't matter as your code shouldn't be looking at that area (unless it has a bug), or unless you have code that expects to be able to write data into the unused pages, and might have problems if there's something already there and they need erasing.
If you were very unlucky and with a non-robust hardware design, then loading "bad code" could drive some output pins to states that caused some short circuits, or drove signals to external hardware that could have damaged it. Nobody can possibly tell if that has happened. it is very unlikely. If you're paranoid, put a label on the hardware listing what happened in case it plays up in the future.
Tom