1. every time the form is submitted.. generate the list of all the
check boxes which are checked and overwrite the previous value in the

2. get the list of all entries from the database see if the
corresponding check box is checked.. if so leave it as it is, if not
remove it...

this depends much on the database implementation. obviously this is a
one to many relationship.
if i use a single field with coma separated values i prefer the former
if i use a different table to store the relationships(one relation per
row) i prefer the later.

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