Again: Zorro will NOT close a virtual trade when a real trade is closed. It is up to the script, by a stop loss or other criteria, to determine when a trade must be closed. Closing a real trade should have no effect on the behavior of a strategy.

Any position difference by externally closing trades, such as that NET:S trade in your step 2), will stay until it is levelled by the strategy. This is perfectly normal behavior as described in the manual, and is no reason to worry.