The same way you accept any contribution, because it isn't technically relicensing. You already granted them an AGPLv3 license when you uploaded your change to github without modifying the license file - that's what the "or" in the file means [1] - which entitles them (and anyone else) to create and distribute derivative works under only the AGPLv3 without any GPLv2 grant...
[1] Quoting the license file:
This software is provided under a dual license. You may choose to use it under the terms of either:
1. GNU General Public License, Version 2 (GPLv2), or
2. GNU Affero General Public License, Version 3 (AGPLv3).