How does DBCC SHRINKFILE() affect backups?
Per Microsoft Support
http://support.microsoft.com/kb/272318, SQL Server shrinks the log file by removing as many VLFs as it can.  It does so while trying to hit a target size without messing up your backup chain.

However, if you do use TRUNCATE_ONLY, the sequence gets messed up, so you'll need to either do that right before your scheduled backup or do full backup right after that.