Thank you for the reply. I managed to fix it late last night.
A few comments though
1) Downloading to 06.08.2 (or 3), was not an option since the affected routers had the MeigLink SLM750 chip. Upgrade message given by the router was incorrect. You cannot downgrade to lower than .5 with that chip.
2) Even though IPSEC was fixed in 07, DDNS was removed, which created some issues since we rely on that. That being said, we found a way to access the routers manually after upgrade, forcing the reinstall and re-adding DDNS again. Luckily the config was still stored.
Hopefully Teltonika will come up with a new 07 release quite quickly that includes DDNS, because upgrading to 07 now is a mess :-)