"Thank you. You're welcome!"
I can't confirm for sure but I believe your sentence is correct. "Nedankinde" means "You are welcome!" As where "Bonvenon" is "welcome". To use "Bonvenon" and choosing to omit "Vi estas" seems fine but adding "Vi estas" should not be wrong. You should report this types of errors for review.
Bonvenon is like welcome to my humble obode, bon.ven.on, bon for good, ven for coming, and on to indicate it's a noun in the acusitive, good comings. Nedankinde is like thankyou, you're welcome, ne.dank.ind.e, ne for no, dank for thanks, ind for required or needed, and e to indicate that it is an adverb, no thanks required.
The -n at the end of bonvenon marks it as accusative, the direct object of a verb. "Esti" is a stative verb, which means it does not take direct objects but rather subject complements.
"Bonvenon" is short for something like "I bid you welcome" or "I wish you welcome" or "I give you welcome". All of these are transitive verbs, which take a direct object.
This is why "Vi estas bonvenon" is wrong.
Also, it would be "Vi estas bonvena".
Also, this can only mean "welcome" as in "welcome to be here". "You're welcome" as a response to "thank you/dankon" is "nedankinde".