He was hosting guests there on Sunday when officials from the Volvo Ocean Race and the Ministry of Economic Development came to serve him a warning.
"They told me, 'You must put down your Waiwera flag because this area'," Mr Khimich said, gesturing across the marina. "They said, 'This area is Coca-Cola territory'."
Mr Khimich was accused of violating the major events advertising rules, which disallow branding in "clean zones" reserved for corporate sponsors.
A fellow Waiwera company director, Irina Nearonova, explained what happened next.
"Of course Mikhail, because he was lacking words at quite an emotional moment, made an 'international gesture'." Police arrived shortly after.
"They threatened us with a fine and said it was a criminal offence," said skipper Luke Tempest.
The officers wanted to come on board but Mr Tempest told them to go get a search warrant.
Coca-Cola was unaware that any action was being taken on its behalf.
"We've got no beef with anybody and it's news to me," the spokeswoman said.
A team of advisers met on board Thalia in the morning to address the situation. The gathering included a lawyer, an events organiser and business partners, who sat around a table on the superyacht's back deck.
The Ocean Race officials arrived close to midday. Mr Khimich emerged periodically with updates, sounding hopeful.
They eventually reached a compromise: Thalia would replace one Waiwera flag with an Ocean Race flag at certain times on Saturday and Sunday, while Waiwera could supply water at Thursday's gala dinner at the Cloud.
The gathering sat down for lunch, where Mr Khimich proposed a toast.
"There are two feelings that progress civilisation," he said through an interpreter. "The feeling of childhood that brings happiness, and the feeling of love which everyone searches for their whole lives. Friendship is like these two feelings, and it is what lasts - even after love."
The group of Mr Khimich's supporters, which had grown to include an event official, held glasses aloft.
"To friendship."