We just applied for FLR for my wife and there was an option to photo copy every page of your passport and not send your passport in. Every page will have your passport number on it so i am sure they can check it is all valid. Here i copy and paste the wording for you.

'Your partner’s immigration status
Your partner’s current passport or travel document showing that he/she is present and settled in the UK. If you are making your application by post you can send a complete and full copy of your partner’s current passport or travel document. Every page of the passport must be copied including any blank pages."