so your doing save as, and saving your modified patch/object into a new location within your own 'local library' e.g. home/objects
my suspicions is the uuid and sha are not being updated correctly.
one thing you could try,
once you have done the save as... hit reload objects... then open up your object in the object editor and hit save again... ( this may correct the uuid... not so sure about the sha, id need to look at that again)
Ive some ideas about how this 'workflow' can be improved that I'm running past Johannes.