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After copying a group of objects (including some containing clipping masks) from Illustrator to InDesign some of the objects disappear after resizing said clipping. My apologies if this is quite vague but to be honest I'm not sure what's happening, just that things are missing. I've recorded a video to better demonstrate what I mean.

https://vimeo.com/83398666

As you can tell in the video, I copied the group of squares from Illustrator to InDesign, then resize the entire group. After resizing, some of the circles in some of the squares are missing. Upon dragging some things around I find one of them and it is still full size (it didn't resize when I dragged the entire group) and it is really far away from its original place. The squares where things are disappearing are all clipping masks (they look different from everything else when I first select the whole group to Cmd + C it).

Thanks a lot for your time and sorry for any bad wording. I'm using Adobe CC.

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Can you explain why you are pasting rather than simply placing the AI file in InDesign? It would also appear as though you're simply using the Selection Tool when resizing, have you tried resizing with the Free Transform Tool? Recent versions of InDesign do odd things when using the selection tool for transformation functions (in spite of what Adobe marketing states). –  Scott Jan 4 at 23:50
    
Hello. The reason I am pasting is because the particular artwork is inside one artboard, where as the AI file is composed of 40+ artboards. I am in fact using the Selection Tool. I've just tried using the Free Transform Tool as you mentioned, and it does not make things disappear - great! (The Scale Tool also worked). Unfortunately though, I could use the Free Transform Tool to make the large resizing changes I wanted, but when I input the exact numbers into the Transform window to make fine adjustments it still made the artwork disappear. (The boxes resize but the circle inside stay put) –  sstaccato Jan 5 at 1:37
    
(continuation) In other words, when changing the numbers in the Transform window, it's as if the borders of the clipping masks within the pasted artwork are resized but the circles inside the clipping masks go unchanged, remaining the same in both size and placement. I'll post another video explaining that. In the meantime, the Free Transform Tool works excellently - it would just be nice to be able to make detailed changes without the artwork disappearing. –  sstaccato Jan 5 at 1:41
    
vimeo.com/83406789 –  sstaccato Jan 5 at 2:00
    
You can easily import only 1 artboard from a multi-artboard AI file. Check the Import Options when placing. I see no viable reason for pasting the artwork. –  Scott Jan 5 at 5:28
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2 Answers

Use File > Place and tick the Image Import Options in the place dialog window before clicking OK. You can then easily import only a single artboard from a multi-artbaord Illustrator file.

While InDesign has some vector tools, much like Photoshop, the core vector capabilities of InDesign are not designed to replace a true vector application such as Illustrator. By placing rather than pasting the image, Indesign treats the image as a container and references the original artwork after transforming (scaling) rather than trying to work out the vector math itself. It's fairly easy to overwhelm InDesign's vector engine with artwork.

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It looks like you aren't selecting the missing objects.

Notice they didn't have the blue outline on them when you selected everything. Make sure your layers aren't locked and as @Scott suggested, save the file and just File > Place it rather than Copy/Pasting.

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Hello. I agree, when I select all the squares certain things don't have a blue outline, but when I paste the selection everything is included. I think the lack of blue outline is because the squares that are causing issues contain clipping masks, the contents of which do not have a blue outline when selected (just the outline of the clipping mask - the square). I'd rather avoid saving each individual (40+) artboard separately but it might be unavoidable. Although the Free Transform Tool doesn't make the contents of the squares disappear, only when manually changing the numbers in 'Transform'. –  sstaccato Jan 5 at 2:57
    
If you're using clipping masks, then you might need to expand appearance. –  OghmaOsiris Jan 5 at 3:11
    
Expand Appearance is greyed out when I select the objects, although I will look into it. –  sstaccato Jan 5 at 4:17
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