P.S. Export and place is the normal process, but on this occassion Id like to be able to edit the layout and content in InDesign. It's a raft of pie charts that cannot be made in InDesign.
By @Will Price
Hi Will
Honestly, I would advise you to save the artwork as AI files and use File > Place instead of copying and pasting.
Let me try simplify my reply a bit here:
When you copy artwork from Illustrator, the swatch information is embedded with the object rather than linked to the document. InDesign then treats this as a separate instance and creates a duplicate swatch even though the colour values are the same.
This issue is compounded by the fact that the two applications handle spot colours, tints and process colours in different ways. The pasted object may use a locally defined swatch that does not match the global swatch already present in your InDesign file. Consequently, any changes you make to the master swatch will not be reflected in the pasted artwork.
In addition, incorporating a lot of editable vector data directly into InDesign can slow down the programme and cause lag when working with complex items like pie charts. By placing the AI file, you ensure that the source file remains linked and any edits made in Illustrator are automatically updated in InDesign. If you need to make changes to the vector file, you can still do so easily by holding the Alt key and double-clicking the placed image, which will open the file in Illustrator for editing.
Using File > Place helps keep your colour workflow tidy and ensures that your source files remain consistent with your InDesign document. This approach not only prevents duplicate swatches from cluttering your palette but also makes global colour adjustments more manageable.
By keeping the source file in AI it also means you can use that asset in other projects, or share them with others who might need to use them as other assets. And you all have the 1 source file that is up to date.
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Is there a way to do what you want?
In illustrator you could make those Swatches Spot Colours

I don't think you need ASE
Then when you paste into InDesign the Swatch is created - so you won't need ASE
Pastes directly into InDesign with the Spot Colour and name

Indesign swatch vs Illustrator Swatch


InDesing go to Ink Manager

I've ticked both options at the bottom

And export to PDF - you also have option for Ink Manager here - changing the ink manager doesn't modify the PDFX4a setting maintaining it's integrity

Result in PDF separations
