Absolutely not, the plugin will operate only on the orders made after its activation.
The plugin has been conceived to offer sequential order IDs: this means that the IDs will continue progressively in any case.
No, the ID will be lost and the new order will use the next number of the sequential numeration.
IDs may be duplicated if you decide to start your numeration with a lesser ID than the one of the last made order. Use prefixes and suffixes to avoid duplicated IDs in your orders.