When a user marks a project for deletion, the delete process / job is not executed.
This can happen if the Delete Projects job (Now renamed to Delete Investments and Time Reporting Periods) is in cancelled status. It's possible an upgrade cancelled this scheduled job, as sometimes when jobs are updated as part of the upgrade, any scheduled instances of those jobs get cancelled and have to be recreated. (See Review Cancelled Jobs After Upgrade.)
Note: There is no out of the box process that will delete projects / investments, this is a job in the system.
Create a new scheduled instance of the job. Below are the steps to schedule the job to run every day at 2:00 am.
You can also run an immediate run of the job to catch up on projects/investments waiting to be deleted.