What are you referring to as 90days? If you held a valid work permit in October and applied for the extension which was refused, it should not necessarily mean that your existing WP is canceled and you have to apply for restoration. In other words, if you applied for a work permit extension again in October after refusal, you did not need a restoration of status as you had a valid status. You went on implied status on January 1, 2019 when your WP expired. Implied status does not expire until CIC makes a decision on your application. You need to make sure that your application was delivered and accepted so you better call IRCC and ask them for your application number and status.
If your current extension gets denied, you will then have 90 days to apply for restoration. But, if your application was never delivered or was returned due to being incomplete, you will be considered out of status from January 2.