Saying this from a respectable distance, but basing my answer on knowing the roads of which you speak I feel safe in saying that the route Mex 200 from Huatulco to Tapachula should experience no significant problems as it is totally on the Pacific side of the mountains .The rains which caused the floods were from an Atlantic side storm and virtually all the major rivers of Tabasco and Chiapas drain back to the Gulf of Mexico.This collects all the water onto the coastal floodplain with the results of this past week.
The route from S.Cristobal to Palenque Mex 199 is a mountain highway and should also be passable, other than a few slides which can occur in any rain event. The region of Chiapas hit with this flooding is also part of this coastal plain and downhill somewhat from Palenque. If I was in your situation I would have no reservations about travelling as far as Palenque, but would avoid the flats for a few weeks till everything gets back to normal. If you travel slowly it should be sorted out by the time you get there.
Check out the Mexican news reports eg Bienvenido a tvazteca.com and TV news reports when in hotels as you progress and adjust route and timing if needed .

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http://advrider.com/index.php?thread....207964/page-5 then scroll down to post #93