Have you tried googling "I thought I have replied"? There are lots of entries for that too. :-D I have seen many entries with "I thought I had replied" too.
That doesn't follow with what the discussion is about because "I thought I have replied" is clearly an error made by an ESL speaker. Extremely infrequent would it be to hear even the least articulate of those native speakers lacking good language skills say something like "I thought I have replied". The reason is that such a combination of two clauses is clearly out of the range of natural native speaker syntax and structures which are learned in a natural way while acquiring English as one's first language.
If you look at this search, it's starts with about 401,000 returns, which by the way pales in the face of the well over 6,000,000 returns for "I thought I replied".
If you click to the next page, for some reason, we see that 401,000 turns into 18. Even on the first page, which is 401,000, it seems easy to identify the writing as non-native speaker writing.
"I thought I have replied" - Google Search
I would take this discussion as a matter of diverse viewpoints among native speaker ELTs. From there, I would observe native speaker usage by listening to the radio, watching films or movies, reading, having conversations - and whatever other way you find to gain exposure to native speaker usage. Take note of how the past perfect and siimple past are used. Ask yourself if one could be interchangeable with the other, and then try to justify why or why not. Draw your own conclusions.
;-)