It doesn't actually synchronise the days, it merely allows you to do so, and enables you to check what day the lot is at. I copy the information from that to the lot load screen, and that's where I store the info on day number, day of the week and season + number of days.
I've never felt the need to uninstall the timer, I would imagine that what he means is that it's the timer that keeps the data for each lot, and the hood, and if you've changed it in any way, then removing the timer from your downloads would mean that the hood would revert to the original day of the week, number of days played, etc., and not the ones you'd set. Removing any adjuster from a downloads folder would have a similar result on whatever they are coded to affect, I would think.