Are both OK:
She invited me over for dinner and made me food when/but she wasn't feeling well and I think that's how she gave the flu to me.
Note punctuation: She invited me over for dinner and made me food when she wasn't feeling well, and I think that's how she gave the flu to me. She invited me over for dinner and made me food, but she wasn't feeling well, and I think that's how she gave the flu to me.
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Note punctuation:
She invited me over for dinner and made me food when she wasn't feeling well, and I think that's how she gave the flu to me.
She invited me over for dinner and made me food, but she wasn't feeling well, and I think that's how she gave the flu to me.