You can do that if you make that backup directory R/W temporarily, however I think it's a risky thing to do. Reason is, that if your Azbox keeps jumping back to the backup, then the odds are good that the sat/channel/transponder data in those 3 .dat files is corrupted, and if you replace the default DVBS.dat file with a now corrupted file, it could mean that the box couldn't recover from errors. I think replacing that backup file might be safe if you're pretty sure that you have files that aren't corrupted, however I think that it's safer, and not much more trouble, to just make routine copies of the 3 .dat files, perhaps once a week, then when the Azbox decides things are corrupted, and reverts to the default backup, you can just replace all three files with the good working files you had from a week ago, and not loose too much, and that process can be done in about 1 minute via FTP.
Anyway, if you have uncorrupted files, the Azbox will generally be pretty stable, and you won't observe problems like described above, and won't need to do the replacing of the DVBS.dat file, and if your files are corrupted and you need to replace that default file, then it isn't safe to replace it, because the file you'd be replacing it with is probably corrupted. So just save a backup. It's easy and safer.