You can easily create a credit note based on an invoice in LSP.expert. When you're in an invoice, you have to click on 'Delete' and select 'With a credit note'.
You'll then arrive in the credit note screen, where you can edit the details of the credit note (and manually change its number format if you wish) and where you can edit the jobs to be comprised in this credit note (using the icons on the right of each line).
You can send this credit note by email by clicking on Actions > Email credit note. You'll arrive in the sending screen where you can edit the text of the email, the name of the PDF file (by clicking on the pencil) and the recipients of the email.
If you want to edit the generic text of the emails you send using LSP.expert, you have to go in Settings > Document and email configuration > Emails tab.
Your credit note will also appear in your list of invoices with a red icon next to it.