I'm pretty sure Tinke can save, you just have to write a new NDS each time. When you replace a file, you'll have to write a new rom, but yeah. I use 0.8.2 for music hacking and replacing SSEQ files, because it can import files larger than what was originally there, which is a major issue with CT.
Useful tutorial nonetheless, it will be useful in many projects. Perhaps what's here can be adopted into a program of sorts.
Also, is there any documentation of this file format in the NITRO SDK? It might have some useful info you could use to expand this.