Change upgrade/install scripts dealing with SQL statements
While parsing the script UpgradeAC7AC708.sql our upgrade became a trainwreck because GIT incorrectly did us a "favor" by changing the line endings to LFs. The upgrade.cs had a line to split the massive script into pieces based on \r\nGO\r\n which no longer matched and cascaded into a myriad of errors. Perhaps you could split on some other characters such as ^^^?
I had our development team review this issue. They pointed me to this article -
Hope it helps.