First question is how good are your backups??????
Never play with raid drives without being sure. Right now I woudln't start any more swapping around until we have an idea of what is happening.
Note that things can go wrong if you have a 2 drive mirror and you boot with a missing drive. Grub expects things in a certain way and removing a drive entirely can have unexpected consequences.
Any drives should be properly failed, or replaced with another drive entirely. You should not just pull one drive and hope it works as it can lead to unintended consequences, as you have discovered.
You should also wipe a drive completely before adding it back - that includes properly clearing the MBR etc other wise it can also have odd consequences.
If you are going to to this you should....
Fail the drive. Shut down. Remove drive. Replace or completely wipe and replace. Reboot. Resync.
Do not be tempted to swap drives about etc. Leave the working one in situ and just replace the 'failed' one. (If you do this on says Raid 5/6/10 etc you will completely trash your array....)
OK. The trouble is now knowing which is the most "up to date" data source?
Curious why it see 3 drives.
What does dmesg tell you?
dmesg |grep sd
And fdisk?
fdisk -l
Or per drive:
fdisk -l /dev/sda
This should show you the same as the raid panel:
cat /proc/mdstat
And then this:
cat /etc/mdadm.conf
Have you got a USB drive or a.n. other drive plugged in my mistake? My son actually had this only a few days ago on a new little server - someone had left a micro USB drive key in a USB socket on the motherboard...