Apps missing after upgrading sd card
I found out that all the apps missing have an .asec file in the .android_secure folder on the sd card, however the .android_secure folder itself is there. 

On Linux I wrote:

cp sdbackup/* /media/disk -r


It copies all folders, and their content, recursively. Except for the hidden folders in sdbackup, e.g.:

sdbackup/.android_secure
sdbackup/.doubleTwist


Hidden folders in the hierarchy are copied however. 

So now I managed by subsequently copying each hidden folder:

cp sdbackup/* /media/disk -r
cp sdbackup/.android_secure* /media/disk -r
cp sdbackup/.astro* /media/disk -r
etc


And now everything is fine.