why am I losing data over serial communication between arduino and pc
Are you hand-typing the commands? It is pretty difficult to do that consistently. I ask because your code collects data from the serial buffer until the buffer is empty - i.e. when you pause even slightly in your typing - and tries to act on whatever it has collected so far. That may be (probably will be!) an incomplete command. Even if your terminal uses line-by-line entry, there is still the risk that your code could notice an empty buffer between characters within a line. 

Try collecting characters until it sees a newline, instead. That is probably what you intended, and it will be immune to your typing speed. You'll still need to test for .available, but that should only allow the code to collect more characters. Keep collecting until it sees a newline.

What (I think) is happening now is called a race-condition. That means that the program's behavior is dependent on which of two (or more) events happens first, and the order of their occurrence is indeterminate. Race conditions are especially hard to find when the order of two events is almost always the one you expected. Notice the "gotcha" word in that sentence? :)