Based on the info so far, there seems to be a couple of unrelated issues that make it appear as though there’s a problem with the -persist option in Duplicacy.
The -persist option is behaving as it should (skipping bad chunks and optionally stopping on existing files unless the -overwrite option is also specified, then it really only ignores bad chunks).
Because Duplicacy generates the filename for a chunk by hashing it contents, the filename is always 63 characters (which is equal to 63 bytes since it only contains the ASCII set).
And because the original filenames are stored in the snapshot log, they aren’t affected by the storage filesystem. Unless the backup chunks are being transferred to a FAT-formatted filesystem (which only supports up to 9 character ASCII filenames), their 63-character filenames are also no problem for pretty much every filesystem created during the past 40 years or so.
Right now the only scenario I can see where Duplicacy aborts with a “Failed to create the file for in-place writing” error during a restore is if the destination is an encrypted directory on the Synology (which uses eCryptfs).