1) Is 400E Compatible with 1000D to backup and restore configuration?
No; as any other scenarios with mixed models, you'll need to adapt configurations or use another available path.
2) How to backup and restore mailboxes of all users from 400E to 1000D?
There's a documented procedure for migration between FMLs and FML and another MTA, using IMAP, it is very straightforward . I used it a couple of times, you'll need some patience waiting syncing mailboxes, but it works.
Look into https://docs.fortinet.com/document/fortimail/6.4.7/administration-guide/326016/migrating-email-from-...
One recommendation: For migration, keeps boths FMLs in the same firmware version
After migrated, take your FML1000D to the version you need.
3) The migration can be one shoot or will be divided into phases of testing?