Hey Nick,
This happened to me when we were climbing in Mexico doing lots of long multi pitch slabs. After about 4 days of this my big toe nails went dark purple/black. They weren't that painful by this time and it didn't really bother me. They stayed that colour until they grew out. Even now they each have a ridge through the middle. I'd say leave them and see what happens. It didn't bother me at all (except when I wanted to where sandals!), they didn't hurt, and didn't fall off.
Cath
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