from what i reading here it seems you want to load in "mywav.wav" amongst others, and edit it etc. then save that as the original file(s) (100% destructive) or if your a little more cautious save to new files.
any editing you do in reaper can be destructively applied with render (to stems - with master mix unticked for multitrack) but this creates new files, which you may find intoxicatingly annoying..
however the sws (b4 beta) now incudes 'autorender', which is basically a one-keypress 'render this region using my last render settings' feature.
you create a region surrounding the edited audio, select the tracks to be saved, hit auto-render and each edited track is rendered/saved according to your render settings and placed in the autorender default render path location, so seperate from project folders or reaper media folders.
using that could take out the PITA of constant render dialogs and file location faffing to destructively apply edits..
though if its just straight editing and no fx, then i tend to just GLUE the items and rename the source take to something descriptive.
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