I really would like to, but I don't really know what I did different last time:
I wanted to do several small modifications to US International KB, so I started creating a bundle from File - New from current input source.
Modified a couple of keys for not to be dead keys and other minor modifications.
Then I saved the layout from File -> save. Only the first time the app ask for a path. There is no save as option.
Imported it in the system using the Organiser, rebooted and selected the KB. My modifications were not working.
So I removed the bundle from the system with the organiser, opened again and my modifications weren't there!
I did a couple of changes and saved again. Opened again and the modifications hadn't been saved.
tried everything without luck: Copying the file manually, looking at the save time (that did not change when saving but did randomly), reading the manual several times.
Tried everything without luck. Then I came to this group and asked for help.
Finally I decided to start from scratch, and as long as I remember I did exactly the same for a second time and this time worked as expected. Why? I really have no clue, sorry.
Thanks for answering.