The Toffees have been accused by their top-flight rivals of making an illegal approach for the Portuguese, who has since departed Vicarage Road and been appointed at Goodison Park.
Silva was brought in by Everton during the summer, four months after being sacked by Watford, but the manner of the Merseyside outfit's initial approach is still under investigation.
Premier League chiefs are pushing for a resolution and, according to The Times, that could mean Everton being docked points in the most serious outcome.
The report indicates that Everton officials, including owner Farhad Moshiri, have handed over phone records and diaries as they are determined to fight off the allegations.
Watford travel to Everton for their first meeting of the season on December 8.