I just battled this for about 30 mins and Google wasn't helpful, so I'm posting here for the next me that encounters this issue...
In short... Penultimate notes that are 200+ pages seem to have issues syncing from penultimate app (ipad for me) to evernote. This shows up as a orange exclamation mark (not red), but it doesn't tell you why.
Here's what I did as workaround:
Split the journal to < 199 pages
Found the point in the penultimate journal where page 200+ started.
Selected all those pages
and copied to new penultimate note.
Named that 2nd journal as a continuation of the 1st, sync'd to Evernote (no problem)
Found the original note in evernote and verified I have now have all content sync'd between first notebook and second notebook above
Renamed original note in evernote to clarify the sync broke
Then just use the 2nd note in penultimate from that point fwd
Clunky but works.
Hope this helps you.
Probalby will NOT come back to monitor replies, but if Google brings you here then good luck on your journey = )