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I can’t speak to Cult of the Reptile God specifically, but there are a handful of things that may need consideration. (Apologies for the wall of text to follow)

Mechanically, monster stats will need some slight tweaking, as AotT uses ascending AC rather than the traditional descending and AC/To-hit bonuses don’t necessarily scale the same as the class/monster attack matrices of old. AotT also has quite simplistic character advancement that doesn’t require gathering gold for XP, so treasure is far less important to the PC and you might consider using “milestone” advancement to ensure the PC levels at about the same pace as the adventure expects (or tack a Gold = XP system onto AotT for the PC and retainers). 

Additionally, there is the the lack of magic-using characters in AotT, which may not matter in low level adventures where 1st level magic-users traditionally don’t have much magic to use, but may be a problem in ones which expect the party to have access to magic abilities. This could be circumvented by the addition of Tech items which perform a similar role to a particular spell/ability. Likewise, magic items present in an adventure could be re-flavored as tech or kept as-is depending on preference, with the Decipher Text skill substituted in to read magic scrolls, and Use Tech to intuit how to use a particular wand. Perhaps a character versed in Runic or Ecclesiastical can simply read and use scrolls as a magic-user or cleric?

Depending on the particular adventure, the Subtlety mechanic may or may not apply at all. In an adventure like Against the Cult of the Reptile God, it could be used to determine if the cult members realize the PC is getting a little too curious and decide to deal with them, or are too oblivious or proud to realize the threat they pose.

Finally, consider that while a 1st level Thone Agent and retainers should be mechanically similar to a party of 1st level adventurers, it’s still only a single player navigating the adventure. Puzzles and challenges that might be trivial to a group of 3 or 4 players, able to bounce ideas off each other and come up with creative solutions, may not be to a single player alone. They might be able to “brute force” some problems with skill rolls, but there may be times where they just get stuck and need a gentle nudge from one of their retainers or another NPC.

Thanks for checking out the game, and if you do end up running Agent of the Throne, please let me know how it goes!