You can have disks in RAID and individual drives as JBOD ("Just a Bunch Of Disks") on the same controller.
I've never heard of a controller adding a drive to a RAID array because it felt like it. You must've done something wrong.
I have 2-4 drives in RAID0 (and RAID5, sometimes) and a few more in JBOD on the same controller on a regular basis. I have taken drives out, put drives in, no problems whatsoever. Information is always preserved, unless you manually specify otherwise.
You always have to manually add a disk to an array. Connecting a drive to a controller configured as RAID never adds that drive to an array. Trust me.
There are a few exceptions. For example there are some controllers that only work as RAID0 or RAID1. This is because their BIOS is controlled directly by the motherboard BIOS though a wizard of some sort. Usually they only accept two disks. For example on some ASUS boards, they have some extra SATA ports that *ONLY* work as RAID. But connecting drives to them never results in the creation of an array, unless you change the settings in the MB BIOS.
Since you can read the disk data in linux, it usually means that you have a corrupted MBR. This can be fixed easily, running two simple commands, but I advise you to backup the data before trying them.
Look on Google for "fixmbr", "fixboot", "bootcfg" and "diskpart" but don't use them if you don't know what you're doing. I won't be responsible for any loss of data.