The option noted will resolve it if unchecked. Generally speaking the experience should be nearly seamless for most users upgrading to 12.9. However, I have seen some sample SQL that contains blank lines within a single statement. Users coding in this style will need to either code differently or uncheck that option. If blank lines in PL/SQL are creating problems then this is a bug. Please report cases here along with a code sample that demonstrates the issue.
Thanks,
Michael