Hi James,
The two missing lines are indeed back (update dated 25/5/2017), but lines 95,122,176,217,254,282,298,356,491,508,617,629 and W9 have disappeared.
Separately, I am again getting a significant number of /Line/Route/Sequence requests with no stop point sequences. This is currently affecting lines 5,8,9,14,21,24,25,34,70,91,98,114,123,132,136,145,148,154,158,183,211,296,307,308,390,397,414,436,486 and 491.These seem to be ephemeral, in that a retry brings back full data.
Here is an example of the returned data for route 5, inbound (tabs and line feeds added for clarity):
{
"$type":“Tfl.Api.Presentation.Entities.RouteSequence, Tfl.Api.Presentation.Entities”,
“lineId”:“5”,
“lineName”:“5”,
“direction”:“inbound”,
“isOutboundOnly”:false,
“mode”:“bus”,
“lineStrings”:[],
“stations”:[],
“stopPointSequences”:[],
“orderedLineRoutes”:
[
{
"$type":“Tfl.Api.Presentation.Entities.OrderedRoute, Tfl.Api.Presentation.Entities”,
“name”:“Canning Town Bus Station 
Romford Market”,
“naptanIds”:
[
“490000039F”,“490011429J”,“490003750L”,“490005902E”,“490008834E”,
“490003551E”,“490011047E”,“490011040E”,“490010201E”,“490016264E”,
“490003273O”,“490013959E”,“490003390E”,“490008601E”,“490003659P”,
“490006360S”,“490010218O”,“490003280X”,“490012843E”,“490004592E”,
“490010408P”,“490003616E”,“490000015K”,“490006734E”,“490008419E”,
“490006700E”,“490003605E1”,“490013653E”,“490004768E”,“490007288E”,
“490003760E”,“490009182E”,“490003535E”,“490009704B”,“490003965E”,
“490006865E”,“490008033N”,“490003762C”,“490003763G”,“490005923R”,
“490003660E”,“490005381E”,“490009090E”,“490005926E”,“490010443E”,
“490005450N”,“490013483N”,“490001243V”,“490014452E”,“490011659L”
],
“serviceType”:“Regular”
}
]
}
Romford Market”,