If you mean the blank.ini, that's one method people are doing to make sure MO2 doesn't get rid of the BaseObjectSwapper folder If you mean the New Text Document.ini in BaseObjectSwapper, yeah that shouldn't be there.
I'm using MO2 and when I try to install gives the "no game data on top level" which is fine, then I righ click in the Data folder (the one with a Checkbox), and right click "Set data directory", but it keeps showing "no game data on top level". If I click OK > Ignore, installs the mod but the mod name shows in Italic and with an "No valid game data" icon
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https://www.nexusmods.com/newvegas/mods/69682
If you mean the New Text Document.ini in BaseObjectSwapper, yeah that shouldn't be there.