Assuming your sql files are located in a folder identified as a resource (eg /src/main/resources), you can specify a different encoding using the maven-resource plugin.
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.5</version>
<configuration>
<encoding>UTF-8</encoding>
</configuration>
</plugin>
</plugins>
...
</build>
And source encoding is specified by the system or manually by something like:
<properties>
<project.build.sourceEncoding>ISO-8859-1</project.build.sourceEncoding>
</properties>
For others that don't know how to do this in Eclipse:
- Window >> Preferences >> General >> Content Types
- Select appropriate content type.
- Specify specific encoding for that content type at bottom of window.