GraphQL files not generated in FlavourBased Project

GraphQL files not generated in FlavourBased Project. It's working fine in 3.0.1v. But it's not building in 3.1.2v.

Steps to reproduce the behavior:
1. Create 2 Flavours, let's say A and B.
2. Put the graphQL files in flavour A.
3. Use AWS version 3.1.2 and Build
4. See the building error.

**Expected behavior:**
All GraphQL files needs to generate.

**Environment:**
- AppSync SDK Version: 3.1.2

Reproduce the build with two flavours, placing GraphQL files in flavour A, using AppSync SDK 3.1.2, and capture the building error. Compare the result with SDK 3.0.1 and trace the GraphQL generation entry point; done means all GraphQL files generate successfully for the flavour-based project.

Written by the indexing model from the issue text.