First, be careful when working with bones - there’s a bug that causes file corruption: https://github.com/synfig/synfig/issues/362
So never try to link bones to anything until this bug is resolved.
Secondly, it’s not the only place where Synfig can corrupt files. Sometimes it happens kind of randomly, but always related to some advanced functionality, such as linking/using converters. If you don’t use that you should be good, theoretically…
Here’s what I do to minimize the damage if I hit some bugs in Synfig:
- Always use cyclic saving. Let’s say you saved your work as MyProjects.sifz file
- Made some changes to it? Save to a new copy named MyProject1.sifz
- Another bunch of changes? Save as MyProject2.sifz and so on…
- When you get to, for example, MyProject4.sifz, overwrite initial MyProjects.sifz file and start over
This way you can always go back if the last file gets corrupted (you have a history of changes). Not sure if it’s helpful, but this is my workflow in Synfig.