do you have MT set to "Annotations Unique per chart" on SETTINGS / CHARTS / GENERAL ?
if they are unique, then each chart has its own drawings, even if two charts are for the same symbol. a "pinned" or linked chart is considered separate from a regular unpinned chart. When you initially pin a chart, MT copies the annotations from the unpinned chart settings to the new pinned one, so you should not lose the settings. Not sure where you would lose stuff. Could you go step by step exactly what you draw and click on to get the lines to disappear and then:
go to FILE / Export Settings.
Leave the checkboxes already checked, and also check LOG FILE.
Export, then email me the exported file please.