Are both the Kobo's authorized to the same Adobe account (for DRM purposes)? If they are, you shouldn't have any problems at all.
If you want to juggle 2 ADE accounts each linked to a different Kobo, then things get a little stickier...
EDIT: Of course, the above is assuming you're talking about DRM-wrapped ADE books. Regular DRM-FREE epubs/pdf's are a non-issue.
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