Q:

IDA fails to recognize the new added segment during execution and seems to think its empty? 

So i dumped a PE file after it was unpacked, but the problem is it references another section in the memory map, so i dumped that section and added it to IDA just like this question :
IDA Pro - Load data in manually created segment
and set the segment as read write, everything seems fine
but it seems like the change is not reflected in the binary during execution, because even tho i can see the segment content and it seems fine, any instruction that tries to access this segment will raise an exception as if there is no segment there : 
456BAD: The instruction at 0x456BAD referenced memory at 0x19A650.  The memory could not be read -> 0019A650 (exc.code c0000005, tid 756)
but even during execution i can see that the content of the memory address 0x19A650 is fine, i think this might be because the binary is not changed or something, but how can i do that?  tried saving patches or reloading the database and saving but didnt work! 
checked the segment access rights and its read write as well

A:

When debugging, IDA uses the actual content of the memory as well as the runtime memory layout and permissions.  If the data you loaded into the IDB is not present at runtime, or loaded at a different address/permissions, it will be ignored.  
Just because you added something to the IDB will not make it appear magically in the debugger, since the OS uses the data from the file on disk and doesn't know anything about IDB.  The only exception to this is the Bochs debugger IDB mode which does use data from IDB, but it's a pretty limited emulation environment which is not suitable for debugging full executables.