I do not understand exactly what you want to achieve, but I will explain the possibilities you have in VM invoice:
1. you can use Invoice ID matching Order ID (you write this is not suitable for you)
2. you can use own invoice numbering ->
there are 2 parameters that control what the next invoice number will be
a) starting invoice ID set in configuration
b) the highest existing invoice ID found in dabase
If a) (configured Invoice ID) is higher than b) (highest existing Invoice ID); the a) value will be used. In other cases b) + 1 value will be used as next Invoice ID.
These are numbered in order as invoices are created = orders change their status. So it is well possible that if order #35 will be confirmed before order #30, the order #35 will be assigned invoice #30 while order #30 will get assigned invoice #31.
So, to start from some point, you can setup the invoice numbering start number e.g. to 1000, and your invoices will be numbered 1000, 1001, 1002, ... in the order of order confirmations.
If you need to reset to 1, you need to delete all existing invioce numbers in database (#__vminvoice_mailsended table) and then regenerate the invoices. (you need to do this manually using some DB manager)