There's a bug in version 3.3.3 and it persists in version 3.3.5.
All the relations stored (in PMA database) for a database are deleted after drop any table of the same database.
It should delete all the relationships concerning the table that you are dropping but it make a delete for all relations stored for the database.
In the Mysql log:
DELETE FROM `phpmyadmin`.`pma_relation` WHERE master_db = 'exampledb'
If you are upgrading phpmyadmin from a prior version you should be carefully, because when you drop any table all you stored relations made before will go away.
I will attach the complete log for making easy to debug the problem.
Apache 2.2, PHP v5.2, Mysql 5.0
Mysql log
Confirmed. Not just the relations but bookmarks also.
Yes, everything in the PMA db concerning the database is deleted, you can see in the logs 8 delete statements associated to the database but without table restriction.
If you don't have a backup of the PMA db you should reconstruct all the relations/bookmarks from scratch and you'll loose history, etc...
Bug was introduced in 3.3.2, it's a side effect of patch #2976790.
Fixed for 3.3.6; not yet fixed for 3.4.x.
Fixed for 3.4.x in master.