I do not understand most of what you say here (and your subsequent replies to yourself). If you are using a "simple text file format", then why are you dealing with binary integer data as if it were 16-bit audio samples?
If you are actually manipulating 16-bit integer values (not strings of digit characters), why do you start with a text file?
As for the kinds of "editing" you want to do (cutting, pasting, scaling, etc), you might need to look at some sort of binary data editing facility that is not tailored to audio data. Tools like Audacity, being focused on audio data, tend to have a lot of built-in assumptions about what "makes sense" for data manipulation, given that it's assumed to be audio. (For example, some operations will impose "dithering" - randomly adding 1 or -1 to each sample value, others will impose various kinds of frequency-domain filtering, etc.)
Since you are not dealing with audio data, those built-in assumptions will have unintended consequences, and might make it impossible to do what you really want to do (whatever that is, really... I still don't understand that part).