Entries missing from indexing (Cindex) software

I am using an indexing software called Cindex to create back-of-the-book style indexes. I save constantly so as not to lose my work, but whenever I check the index file against a backup I exported to Pages, there are huge swathes that are missing. If this is an iCloud issue, is there any way to retrieve my work? Is there any way to prevent this from happening again?

Thanks