moving SD card in and out without messing up apps in it

I always leave my SD card inside my phone, but yesterday I had to use it in a Galaxy Mini 2 to install a custom ROM.

As I put it in my own phone, all apps which where installed in the SD card where missing ("App isn't installed") fortunately my data was not corrupted, but I move my SD often and I'd like to avoid this kind of problems. How can I do that?

Also, I'd like to notice that the custom CWM was buggy (in fact the samsung was bricked), but I don't believe that's the cause.

thank you in advance! PS: I'm sure this is a copy of an older question, but I can't find anything similar