When you use a Flag field in Microsoft Project, the default setting is N. I was asked recently if this could be changed to a blank. It can’t if you use a Flag field.
However, you could instead create a Text field and just have the Value X which can be found from a dropdown, otherwise the cell will be left blank.
To do this, on the Project tab, in the Properties group, click Custom Fields. The Custom Fields dialog box will be displayed.
Ensure Type is set to Text then in the Field selection, click on an unused Text field and click Rename to give it a sensible name. Click OK.
Now click Lookup. Type Y as the Value on the top row. Click OK twice.
Now insert the column into the relevant table in your project. Everything will initially be set as a blank. There will be a dropdown from which you can select Y as required for the various tasks.