As the article states, this issue was observed between 2009 and 2013, so is not current anymore. It relied mainly on two things:
- According to the anonymous Kaspersky employees, because other anti-virus software editor were allegedly copying, "stealing" Kaspersky technology,
- And in all case with more certitude because there was at least during this period a real marketing race to which editor was the first to detect an infected file and to detect the largest amount of them.
The trick was therefore relatively simple: submit some code sample to VirusTotal which will be flagged as malicious by Kaspersky alone, and the other editors will soon "catch up" by updating their signature base to include this one as well. The most technically difficult part was to manipulate other editor's software into producing a signature matching also legitimate files.
IMHO this showed a very poor approach where marketing takes precedence over security.
This article also explains how such deception practice were discovered by the anti-virus companies (for instance a sudden rise of customers calling the AV support because their printer's driver has been quarantined), and how they saw this as a flaw in their anti-virus software and signature management processes to be fixed.
So these software and processes being (theorically at least!) harder to corrupt nowadays, such flaw should not happen anymore and, therefore, to answer your question you should not worry anymore.
At the time of such practice was observed however, the anti-virus would not clean the file but quarantine or delete it because its code matches a pattern wrongly flagged as suspicious. There is indeed nothing to clean, the file being a legitimate one! The "bad code" was only injected in the initial sample sent to VirusTotal in a way that competitors will not add the bad code to their signature base, but the legitimate one...