Hmmm, A quick look at the code and it looks like that the migrate script redirects to the bigdump.php file to handle the data import. Migrate seems to have lib-common.php loaded (which is were the function COM_nl2br is located) but bigdump does not. Bigdump.php only has the one com_ function call to lib-common.
The configuration doesn't seem to be loaded so we don't know the html path to lib-common.php so you have 2 options.
1) Either load the database yourself with your backup and run the migration that way
2) Change line 271 to
PHP Formatted Code
INST_getAlertMsg($LANG_BIGDUMP . $linenumber . ': ' . trim($dumpline) . '.<br ' .
XHTML . '>' . $LANG_BIGDUMP . trim(htmlentities($query)) . '<br ' .
XHTML . '>' . $LANG_BIGDUMP . mysql_error());
Either option should get you around the problem (but not really fix it).
One of the Geeklog Core Developers.