Backup & Migrate: Restored changes lost after clearing cache
Sorry, but your approach is wrong.

If things gets to disappear after cache clear, you have some serious bug in your implementation.


You should exclude all cache tables from migration.
After migration, you should clear cache of recipient site.


If your procedure is different, it's buggy. Details may vary but these two points are pretty much needed for consistent workflow.

If one of your sites generates different menu than the other after cache clear, then you failed to migrate some files that provide hook_menu or hook_menu_alter, or you have a problem with migrating menu data in database. Either way, disable cache for migration, don't ever try to rely on migrated cache.