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How are you annotating? Are you using the tool or are you manually chaining the names?
If you are just dragging component from a library and they all have the same designator (U1) you need to change the default designator in the library to "U?".
Then you can use the annotation tool to automatically annotate the schematic.
Somehow there are two "R22"'s in the schematic.....can i somehow click one and get it to change to an "R" number thats not already in use?
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Actually, ive just noticed there are multiple components with the same designator...do you know how to change it so all the designators are different?
I am not sure if this shoudl even be possible at all....seems like a bug?...this never happens in eagle pro