I'm sure some more experienced people will give you better advice, but I've had a similar thing and have had to skip a week of training. My plan is to ease back in with gentle runs rather than just going straight for the next run in the programme. I'm following a P&D schedule and they've got a reassuring table of what to do if you have to take time out:
Number of days missed: 8 weeks or more till marathon: Less than 8 weeks:
fewer than 10 resume schedule resume schedule
10 to 20 resume schedule revise goal
more than 20 Revise goal Revise goal
I'm interpreting that as: if you're not sure you're fully recovered yet, there's still plenty of time to get back into training without feeling like it'll be a disaster if you miss a bit more of the schedule.
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