Safely making truffle honey
Botulism is spot on - not only can botulism spores survive in honey (hence the "no honey for babies under 1 year" rule), the truffles have grown in soil, which is a typical source of Clostridium botulinum spores.

There are well- known reports of botulism caused by garlic in oil and truffles in oil (albeit rarer due to the way smaller total amount of truffles used), honey is in that respect very similar to oil: anaerobic and low-accidic. So although I found no explicitly mentioned case of botulism caused by truffle honey, the general safety rules for preventing botulism should be applied. While honey has certain antibacterial properties, they do not affect botulism spores.

With C. botulinum you have to keep three temperatures in mind:


85°C / 185°F
At this temperature, live cells die.
100°C / 212°F
A few minutes at this temperature destroy the toxins. 
121°C / 250°F
A few minutes kills C. botulinum spores.


Now a short evaluation of some recipes I found during a cursory Internet search:

Most recommend adding the shaved or chopped truffles to the honey and heating the mixture in a water bath or similar to 85C for a few minutes (5-15).

Keeping in mind that neither truffles nor honey are substances C. botulinum can feast and grow on in abundance - and hence are not exactly ladden with toxins - and that the truffles neither grew in nor typically were stored in anaerobic conditions, this step will be safe enough for immediate consumption of the truffle honey and short-term storage.

However, this will not kill the C. botulinum spores, which can germinate and grow in your non-sour, anaerobic environement in your honey jar, especially if stored at room temperature. (Storing your honey in a refrigerator will extend the time until you reach a critical mass considerably, but I can't give you a precise formula. One source mentioned one month in a refrigerator for home-made truffle oil prepared by this method, but as I couldn't verify this claim I can not comment on the correctness of this claim.)

If you want to play it really safe, you need to either 


lower the ph to below 4.5, (which is not feasible for truffle honey) or
seal the jars and heat the mixture to at least 121 C / 250F for at least three minutes (which is usually not possible in home environement unless you have pressure canning equipment) or
heat the sealed jars to 100C / 212F (boiling water) for at least five minutes and repeat this after a day or two to kill leftover spores that have germinated in the mean time. This is known as Botulinum Cook and is safe even for very susceptible products like meat. This leaves your jars safe for long-term storage at room temperature.


Find a paper on these guidelines and thresholds for example here (issued by the NZ governement).