Issue with the Apps that are installed on SD Card after reinserting the SD Card

I am using an Xperia X10 mini pro (Android 2.1-update1). I rooted the phone and partitioned the 8GB SD Card into two parts. 1. ext3 2. FAT32. I installed Link2SD to move the apps to SD Card. This has been very useful as this application has an option to move the installed/updated apps to SD Card automatically. But recently it happened to remove my SD Card from phone and inserted another 2GB SD Card for some other purpose. I started the phone and the apps that are showing on phone aren't working as I installed them on my SD card. So I put my 8 GB Micro SD card back to phone. Now the problem arose. I was not able to access the apps installed on SD Card. I had to reinstall all the apps that are there in my phone. Is it how it behaves ? Don't I remove my SD card from phone ? I did a little amount of Experimenting on this and found that its happening only on inserting another SD Card. My mobile is searching for the apps on the newly inserted SD Card. As there are no apps found it might be deleting the links on phone memory. This is my guess only. Still the question stays "How to overcome this kind of scenario ?"