Nevermind, the solution was deleting the file and replacing it with another one with the same name

Also, all 3 beans must use the @Primary annotation in the main DB

@Configuration
@EnableJpaRepositories(
    basePackages = ["mx.collia.api.maintenance.repository"], 
    entityManagerFactoryRef = "maintenanceEntityManagerFactory", 
    transactionManagerRef = "maintenanceTransactionManager")
class MaintenanceDBConfig {
    @Bean
    @Primary
    @ConfigurationProperties(prefix = "maintenance.datasource")
    fun maintenanceDataSource(): DataSource {
        println("Maintenance DB Config Loaded")
        return DataSourceBuilder.create().build()
    }

    @Bean
    @Primary
    fun maintenanceEntityManagerFactory(builder: EntityManagerFactoryBuilder, @Qualifier("maintenanceDataSource") dataSource: DataSource): LocalContainerEntityManagerFactoryBean {
        return builder.dataSource(dataSource).packages("mx.collia.api.maintenance.model").persistenceUnit("maintenance").build()
    }

    @Bean
    @Primary
    fun maintenanceTransactionManager(@Qualifier("maintenanceEntityManagerFactory") emf: EntityManagerFactory): PlatformTransactionManager {
        return JpaTransactionManager(emf)
    }
}