Flasks do get scuffed up from normal use. NaOH has a tendency to exacerbate this. You could try cleaning with vinegar and rinse with acetone/alcohol make sure what you are cleaning with good contact on the area.
Your flask is fine for future use more than likely. Make sure they are not cracks and are indeed only scratches
. Sillicates are insoluble in nonpolar solvents so your dmt should be safe from the milligram that may be missing.
Where you heating this flask simultaneously(such as a hot-plate)?