Unfortunately AttSync is an all-or-nothing sychronization command. It will change all properties of all attributes in all references of the block to match the AttDef's in the block definition. So if you have some references with moved, or otherwise altered attributes, these modifications would be lost. The only data not lost through AttSync is the text inside the attribute references (if the attribute wasn't renamed).
The only way I can think of circumventing this would be to save the modifications into a list. Then after applying AttSync re-modify the attributes back to their original positions, rotations, scale factors, properties, etc. BTW, this also applies to attributes in mirrored blocks - using AttSync on mirrored blocks would cause the attribute references to display back-to-front.