Let's say you have a Pro Tools session with Markers placed for verses, choruses, etc... You're working in Shuffle mode and need to make an edit that involves removing a few bars from a verse, but when you cut out the section you want to remove the audio shifts to the correct position but the Markers do not. This causes the Markers to no longer line up to the parts of the song they are supposed to mark.

The solution is to Shift-click on the Marker ruler after you make the edit selection in the Edit window. In other words, use the Selector tool to highlight the audio you're removing and then Shift-click on the Marker ruler. When you hit delete, the audio AND the Markers should shift to the left.