Took me awhile to remember what I did about pens last time it came up for me. We ended up labeling a number of metal clipboards and using those bank style pens with sticky bases and chains to keep them attached to clipboards. Clipboards were checked at end of shift, operators had to report if a chain broke or any part of the pen was chipped. The pens weren't sold as "metal detectable", so I did a test on my own that the pens indeed would trip every detector in our plant. This appeased a couple years' worth of SQF auditors while I was at that plant.
I don't know about including them on a register, since that seems like you'd have to have a controlled number of them at any given time and maybe even uniquely identified (Pen 1, Pen 2, etc).