[kiwidude]

The issue of broken anchor links where they consist of an href without a file prefix is really a bug/limitation in Sigil (that also occurred in 0.5.3). I will take a look at how easy that is to fix. Any valid anchor links which are fully quallified with a filename should be preserved no matter what split, merge or rename operations you perform, but this is one edge case which has been missed.

The other known case is NCX links not surviving merge operations, but that is intentional for the moment.

Edit: Actually I thought I had replicated a splitting issue like the OP posted, but subsequently realised it is actually behaving correctly (my href was to a different id than the one I thought, thereby being on the same page after the split and hence untouched). So if you are able to come up with a repro case where splitting does indeed break initially valid links then I would be interested to see it.