A small 'test case, would have been nice .. and “it doesn't work, for some odd reason” does not tell much. What EXACTLY happens. We cannot advice from the knowledge on what does not happen – we need to know what does happen!
If the INSERT statements are in the form ('full inserts')
INSERT INTO tablename (col1,col2,..,coln) values (val1,val2,..,valn)
.. it should work. The short form
INSERT INTO tablename values (val1,val2,..,valn)
won't if structure was changed
But why do'nt you not just ALTER TABLE form SQLyog when you need to add columns ???