Syd,
As far as I am aware nothing else has went wrong. Some of the routes you detail KLM65T for example has been added back into the d/d 5 or 6 times in the last week and gets deleted each time on the following occasion the flight is picked up. The ones on your post were checked and were re-entered where necessary and only a few of the BEE ones were again deleted when I checked them a short time ago and have again been re-entered.
I have not have a response as yet from Airnav but as Dev is out of reach for a good part of each day I expect one when he is able to email.
In addition to the initial entry of the route details and to try and maximise these details within the Navdata, prior to each Navsata being run, Orkney at my request does a mass PHP input into the d/b of all the RYR, EZY, EZS, and TUI routes and all CFE, BAW and Thomson alpha numeric routes. Therafter I have kept a copy of all routes processed in the last 7-8 weeks or so and again before the Navdata is run off, I manually re-enter these again, a process that takes me a couple of hours to complete.
I have entered around 37,000 routes into the database and if I was to include all the re-entries of the ones I note as having gone missing each day it would probably be around half that again.
Alan