Have you had previous supply problems? If not, I wouldn't worry too much. Your body is pretty clever and mostly will be able to deal with changes like that. Babies often go through phases of nursing less often e.g. teething or the many little bugs they can pick up. When your LO is feeling better, you may find she wants to BF a lot, like the early days of cluster feeding, to boost your supply back up, but she will be fine as your boobs can make more milk as she's feeding so you're never really 'empty'. If you just let her feed as she needs, she will get your supply back to normal fairly quickly, assuming you don't normally have supply issues.
If your manual pump isn't working to get some milk for her to drink now, have you tried hand expressing? I find it much more effective.