Hi Monika,
IMHO, I do not think that the diethyl phosphite will silylate, as there is too much steric hindrance around the phosphorous atom (in the five oxidation state I am assuming?, as the three oxidation state will silylate).
AT-1 is 100% DimethylPolysilioxane, the BSTFA will not affect it, if anything it would silylate any active sites in the liner and column.
If peak tailing is not an issue (integration), then don't worry about the column. Are they using an internal standard to minimise reproducibility errors (eg varying injection volume), or, if they inject the same sample 20 times and plot the area, does the area integrated over subsequent injections drop. As you can't just calculated %RSD and state that there is a problem. As it could well be that there is an issue with the injection port, and injecting twice the volume with a 1:1 split will increase the linear flow and deposit your analyte onto the column faster, so that you can open the split vent sooner to flush the liner, and reduce peak tailing.
The only reason why I mentioned injecting BSTFA to clean the detector is purely speculative, and if I was
to have a bet, then I would think that any phosphate stuck to a detector @ 250'C will need mechanical removal as it has baked itself into that crystalline state, and the probability of enough of the BSTFA that would survive the combustion process in the FID AND find its self to the Phosphite is minimal IMHO, the greater effect would potentially come from the HF that gets generated because of the combustion, and as the HF is generated after the column, if doesn't destroy the column. (of course the instrument should already have any combustion products being ventilated away properly).
You also need to ask what part of the FID is being cleaned, as I'm guessing it would be the jet & not the collector.
Alex