First of all, importing from the same module with different prefixes may be violating the Yang standard, although the relevant sentence is not very explicit:

Multiple "import" statements may be specified to import from different modules.
https://tools.ietf.org/html/rfc6020#section-7.1.5

Anyway, current ODL behavior differs on which prefix is then used. Here are simple test models: https://git.opendaylight.org/gerrit/#/c/41269/1

Ideally, parser could support multiple prefixes pointing to the same imported model.
If that is not easy to implement, parser should at least produce an Exception with a message informing about multiple import from the same module.

Currently the exception only informs about not finding the desired node:

[ERROR] yang-to-sources: Unable to parse yang files from /home/odl/build/mdsal/model/test/bug-augment/src/main/yang
java.lang.IllegalArgumentException: Failed to parse node 'bt0:target' in path '/bt0:target'
at org.opendaylight.yangtools.yang.parser.stmt.rfc6020.Utils.nodeIdentifierFromPath(Utils.java:452)
at org.opendaylight.yangtools.yang.parser.stmt.rfc6020.AugmentStatementImpl$Definition.parseArgumentValue(AugmentStatementImpl.java:75)
at org.opendaylight.yangtools.yang.parser.stmt.rfc6020.AugmentStatementImpl$Definition.parseArgumentValue(AugmentStatementImpl.java:62)
at org.opendaylight.yangtools.yang.parser.stmt.reactor.StatementDefinitionContext.parseArgumentValue(StatementDefinitionContext.java:34)
at org.opendaylight.yangtools.yang.parser.stmt.reactor.SubstatementContext.<init>(SubstatementContext.java:47)
at org.opendaylight.yangtools.yang.parser.stmt.reactor.StatementContextBase$1.build(StatementContextBase.java:327)
at org.opendaylight.yangtools.yang.parser.stmt.reactor.StatementContextWriter.defferedCreate(StatementContextWriter.java:45)
at org.opendaylight.yangtools.yang.parser.stmt.reactor.StatementContextWriter.startStatement(StatementContextWriter.java:32)
at org.opendaylight.yangtools.yang.parser.impl.YangStatementParserListenerImpl.enterStatement(YangStatementParserListenerImpl.java:82)
at org.opendaylight.yangtools.antlrv4.code.gen.YangStatementParser$StatementContext.enterRule(YangStatementParser.java:113)
at org.antlr.v4.runtime.tree.ParseTreeWalker.enterRule(ParseTreeWalker.java:66)
at org.antlr.v4.runtime.tree.ParseTreeWalker.walk(ParseTreeWalker.java:49)
at org.antlr.v4.runtime.tree.ParseTreeWalker.walk(ParseTreeWalker.java:52)
at org.antlr.v4.runtime.tree.ParseTreeWalker.walk(ParseTreeWalker.java:52)
at org.opendaylight.yangtools.yang.parser.stmt.rfc6020.YangStatementSourceImpl.writeFull(YangStatementSourceImpl.java:98)
at org.opendaylight.yangtools.yang.parser.stmt.reactor.SourceSpecificContext.loadStatements(SourceSpecificContext.java:329)
at org.opendaylight.yangtools.yang.parser.stmt.reactor.BuildGlobalContext.loadPhaseStatements(BuildGlobalContext.java:228)
at org.opendaylight.yangtools.yang.parser.stmt.reactor.BuildGlobalContext.buildEffective(BuildGlobalContext.java:196)
at org.opendaylight.yangtools.yang.parser.stmt.reactor.CrossSourceStatementReactor$BuildAction.buildEffective(CrossSourceStatementReactor.java:134)
at org.opendaylight.yangtools.yang.parser.stmt.reactor.CrossSourceStatementReactor$BuildAction.buildEffective(CrossSourceStatementReactor.java:151)
at org.opendaylight.yangtools.yang2sources.plugin.YangToSourcesProcessor.processYang(YangToSourcesProcessor.java:177)
at org.opendaylight.yangtools.yang2sources.plugin.YangToSourcesProcessor.execute(YangToSourcesProcessor.java:93)
at org.opendaylight.yangtools.yang2sources.plugin.YangToSourcesProcessor.conditionalExecute(YangToSourcesProcessor.java:104)
at org.opendaylight.yangtools.yang2sources.plugin.YangToSourcesMojo.execute(YangToSourcesMojo.java:119)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: java.lang.IllegalArgumentException: Error in module 'bug-augment': can not resolve QNameModule for 'bt0:target'. Statement source at META-INF/yang/bug-augment.yang:14:2
at com.google.common.base.Preconditions.checkArgument(Preconditions.java:145)
at org.opendaylight.yangtools.yang.parser.stmt.rfc6020.Utils.qNameFromArgument(Utils.java:516)
at org.opendaylight.yangtools.yang.parser.stmt.rfc6020.Utils.nodeIdentifierFromPath(Utils.java:448)
... 45 more