Thanks for the help.  I eventually figured this out given the points above. 
I simply output the open address and close address of each database I opened
and closed to see if something wasn't being closed. 

It turned out to be a far more simple problem in the end.  A silly one at
that.

I was testing the closed state of a database like this.  After it closed on
the first instance it would try to close the database two more times which
is why the SQLITE_MISUSE error kept appearing.  Once that started I couldn't
delete anything.  

Just a stupid programming error as I suspected.   No I just test the state
of the database once and then test the output in my if statement. 

if(sqlite3_close(.......))
{

}
else if(sqlite3_close(......))
{

}
else if(sqlite3_close(......))
{

}



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