When you use the "save" option, the program saves to the last edited/opened file. "Save as" saves a fresh file under a different name. Using "save" after using "save as" will cause the program to save in the new file location, like using "load" then "save" will save to the loaded location, even when the file name is "_autosave########.an8". Using the "save" option is fine, you just have to be wary of where it is saving to.
From your first post it sounded like you lost all the progress from the point on from the bone influences. If everything else you did stayed then I'm less sure of what the problem is.
Did you edit the mesh or figure in any way, as many/most every way that does destroys bone influences from what I've done, and heard of.
Did you have multiple files saved including quicksaves? It's often easy to misplace progress if you load or save where you did not intend. Try saving to a new location and opening that file, after making some simple bone influence edits. If it's a saving error with the old file, perhaps anim8or is having issues with the file being partially corrupt, and saving to a fresh file will fix it.
Did other files you have end up with the same problem as well?
Edit:I just loaded a file up of my own, and the bone influences are working fine for me on the saving/loading end...