David, no ultimate answers but some ideas.

I've just had comparable issues on a mirror with all the maintenance tools not 
working as expected. I my case the problem came down to 1- a bad power cable to 
one of the disks loosing contact once in a while, 2- a non-locking SATA cable 
that came out ever so little from the socket. Luckily both were focussed on the 
same physical drive. 

My BIOS mostly showed both disks. Only once one drive was missing leading to 
the power supply. 'format' always (!) showed both disks of the mirror. 

You ask about the effect of the commands logical vs. physical. My understanding 
is that they are simply tools for the handling of how the OS sees the drives. 
So a logical level within the pools. 'zpool replace' (see 'man zpool') allows 
you to logically replace the drive in the pool. As it carries out the 
resilvering, both, the old and new physical disk have to be present in the 
system. At least that is how I understand the 'replace' option.

>From the man pages:

zpool replace [-f] pool old_device [new_device]
replaces old_device with new_device. This is  equivalent
to attaching new_device, waiting for it to resilver, and
then detaching old_device

Since you should not remove physical devices from a zpool without telling the 
OS something about it you need to use 'zpool detach' (or similar).

Trying to attach my badly connected drive led the 'zpool attach mypool drive' 
command to tell me about using fdisk and slices. Rather misleading, maybe like 
what you are seeing.

Regarding the extra space used. I just posted a similar question: 
http://www.opensolaris.org/jive/thread.jspa?threadID=114104&tstart=0

Though I have no idea how that fits to the initial problem, if at all, never 
mind where that data is...
Maybe you could post your 'df -h' and 'zfs list' output? 

Hope this helps a bit,
Martin
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