Since SU7, IFR flight plans for the WT CJ4 created using LittleNavMap, that have worked perfectly for months,
can be loaded into the sim using the World Map and then into the FMS, but they no longer work in NAV AP?
All of the legs are present and everything looks OK. There is simply no NAV.
In another forum they stated that SimBrief flight plans are the only ones that still work.
Has anyone else encountered this?

Same for me. I get the magenta line but they are kinda...inverted to me but reversing them back again won't work. I'm personally not gonna use SimBrief 'cause of the Navigraph sign up. Ok,it's not mandatory but...Let's hope for a LIttleNavmap update.😔

simBrief might be fine for commercial routes, but it doesn't appear to have the features needed for sightseeing remote locations. I guess I'll be flying the Heading Bug and use the FMS for altitude.
I think the problem lays at Asobo's feet for the FMS. 
LNM works fine. The World Map loads the flight plan and the FMS loads the flight plan. The FMS just doesn't use it?
The FMS NAV doesn't work with flight plans made using the World Map either.
I read somewhere that Working Title uses the stock FMS in its CJ4.

3 hours ago, Stu52 said:

I read somewhere that Working Title uses the stock FMS in its CJ4.

Here's what the WT CJ4 changelog page says about the FMS

FMS - Rockwell Collins Pro Line 21 represented at over 75% accuracy
Over 40 screens/pages of the FMS have been developed
Route planning complete with departure and arrival procedures, airways and direct waypoints, including many procedures and procedure types missing from the default aircraft
Performance init pages including complete takeoff and approach performance calculations, with field lengths and Vspeeds
Custom developed and implemented a flight plan import directly from Simbrief via the FMS, allowing users to spawn without a flight plan, then load a Simbrief OFP/Flight Plan directly over the web (requires internet connection); this feature also makes it easier to fly multiple legs without exiting the simulation session
Custom LNAV and VNAV capabilties reflective of the real aircraft’s capabilities
Improved performance of FMS by streamlining data access behind the code
Added custom mechanism for saving and storing default settings to remain persistent between sim sessions
Added transponder functionality and completely redesigned the TUN page for radio tuning

It doesn't seem like the stock FMS.....

When I realized the problem was with the sim and not the WT CJ4 or Little NavMap, I broadened my search criteria and found
a post that by a fellow who said he restored NAV operation by changing the Flight Model from Modern to Legacy.
It worked! I just completed a WT CJ4 flight from KBOS to KJFK using a plan created in the World Map. 
The ILS Approach also worked.   

this is a shame. is anyone else able to get the WT CJ4 to work now?

dresoccer4 - WT CJ4 flies fime. The FMS is a bit finicky with the source of flight plans for ILS NAV.
It sounds like SimBrief is best. World Map works. Waypoints in Little NavMap show on the Map but may not be followed by NAV.