I could reproduce the problem, and somewhat reduce it:

It looks like lines that contain a \n just before the semi column are
ignored. oO

Example with sql files:

This works:
-- 8< ---------------------
delete from translations where lang='en' and internal=1;
-- 8< ---------------------


This doesn't work:
-- 8< ---------------------
delete from translations where lang='en' and internal=1
;
-- 8< ---------------------


But this works:
-- 8< ---------------------
delete from translations where lang='en'
and internal=1;
-- 8< ---------------------



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