What issues must be taken into account when doing this?
Yes, this is possible. There are two potential issues with flexible packaging. The first involves the material of which the packaging is made. If the packaging is foil, then the metal in the foil will affect your ability to read tags. If a tag is inside a foil liner, the energy will not penetrate the liner and the tag will not be interrogated. You would need to put the tag on the outside, which might look unattractive, unless the tag were designed into the package.
The other issue with flexible packing is the potential to bend the tag and break the connection between its chip and antenna. This would render the tag inoperable. To prevent this from happening, you could use a substrate thick enough to protect the tag but thin enough to allow it to bend with the packaging. The substrate could be thicker near the chip to protect the connection, which would allow the antenna to bend with the packaging without breaking that connection.
—Mark Roberti, Founder and Editor, RFID Journal
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