Ignored Lines in my GEDCOM file

This may not be true.

Those lines meant the GEDCOM line was unrecognizable to the importer plugin but would probably be recognizable to a human.

So a note was created with that tag, its data and and what fault occurred. Gramps goes to painful lengths to create such notes to do the exact opposite of blindly discarding potentially useful data.

You may have deleted 100,000 line of real data … but we cannot tell from your description.