SQLite Forum

How to remove a column and guide from the docs
Your problem is not with the process which is removing the column.  Your problem is that some other process is accessing the same database and hasn't finished whatever it's doing.

A common cause of this is reading a set of rows from the database using <code>SELECT</code> and not using the API call which tells SQLite that you're finished with that set of rows.  The connection stays open even if SQLite has told you there are no more rows of data to return.  Under normal circumstances the connection remains live until the application quits, and doesn't affect anything else.  But in this specific case you're making a change which affects the way the database is organised, so SQLite is insisting that nothing else is accessing the database while that happens.

Try rebooting, then immediately making that change before anything else accesses the database.  Does it work ?

And as was commented upthread your OS probably provides a way for you to see which processes are accessing a specific file.  You can use that to figure out which process is not properly terminating its access when its finished with the data.