In Expeditionpcb's forward annotation, there is an option "annotate schematics reference desinator chages", if you click it on, all your placment and routed traces
will not losted after eco-annotation even your refs and netnames changed.
We love Expditionpcb's intelligence annotation.
Packager provides several options with how it handles data update from the library, if you use 'Update Local Library Data with newer central library data', then the tool will update the definition of the FPGA without affecting other unchanged parts, you can also control what the packager will do, default is to 'Package Symbols' which will package unpackaged symbols and leave the rest alone, other options are 'Repackage All' which will (potentially) change existing references. 'Package Symbols' with 'Update Local Library Data with newer central library data' should do what you want.
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