You have to be sure to be referencing both function library files in the test. There are 4 main ways to do this.
1. Go to 'File > Settings > Resources > Associate Function Library' and associate both library files
2. Use AOM Code
3. Use ExecuteFile method somewhere in the script
4. Use LoadFunctionLibrary method somewhere in the script
(examples borrowed from (http://www.automationrepository.com/2011/09/associate-function-library-to-qtp-script/)
Set objQTP = CreateObject(''QuickTest.Application'')
objQTP.Visible = True
'Open a test and associate a function library to the test
objQTP.Open ''C:AutomationSampleTest'', False, False
Set objLib = objQTP.Test.Settings.Resources.Libraries
'If the library is not already associated with the test case, associate it..
If objLib.Find(''C:SampleFunctionLibrary.vbs'') = -1 Then ' If library is not already added
objLib.Add ''C:SampleFunctionLibrary.vbs'', 1 ' Associate the library to the test case
LoadFunctionLibrary ''C:YourFunctionLibrary_1.vbs'' 'Associate a single function library
LoadFunctionLibrary ''C:FuncLib_1.vbs'', ''C:FuncLib_2.vbs'' 'Associate more than 1