Ok, so what you need to do is called a "retag".  You need to boot to CTRL-R and write down the settings for your RAID 5 (size, stripe size, etc.), then delete your RAID 5.  Then configure your RAID 5 again, using the exact same settings, but do NOT check the Advanced (or Initialize) box.  Then immediately force offline disk 3.  Try to boot to see if it works.
I have been reading the forums and this seems it might be a lost cause, but I am posting hopefully to fix this.  Our server is not hot swapable due to the mounting configuration in the system.  We have to pull all the drives out to get one access to one.  While removing the bad drive to get the information for replacement, we had to unplug all the cables.  During the restart process one drive came up as a foreign disk.  "We" cleared the foreign disk, and now the server will not boot, nor will it let me add the disk back to the raid. With only three functioning disks, and now one of those was removed, we only have two that show up in the controller card as online.  the raid is offline and I fear we are going to have to rebuild everything. As far as I know, there are no backups to this server.  The data is not hugely important, but the time spent in bringing this thing up was a huge labor cost.  I hate to toss that money out the window.  Is there any hope of undoing the clearing of the foreign disk? If so how would I need to do that?
Dell Poweredge 1900 Raid5 accidentally cleared foreign disk