Did you use the cache-line flush instructions directly or use some higher-level package from the PMDK for adding byte-addressable NVM support to LMDB?

Nope, nor was any of that necessary. LMDB works reliably with Optane DIMMs already, unmodified, by default. By default, LMDB uses a read-only mmap and write() syscalls, so it's the OS's job to persist the data. If you used the MDB_WRITEMAP option to write through the mmap, then you would indeed need to add explicit cache-line flush instructions. But that's not the recommended way to use LMDB.