I know we're supposed to use 5-15 Syns per day and I usually do, however out of my total Syns allowance over the past week (105 Syns) I've only used 99.5
Should I use up the remaining 5.5 or leave them as they are ?

If you don't want them don't have them.
You should never feel like you have to use the full 105 a week, but SW advise that you use at least some every day. They're there to be used when needed and wanted, but don't ever feel like you HAVE to use all your Syns if you don't want them x

It wouldn't sabotage my weight loss if I did though?

No not at all, like I said they're there to be used. If you want to use them go for it x