You can get the sqlagent job steps information by querying the msdb tables. In that, you can find out, which configuration file is being used in the job step.
Refer to sql agent jobs documentation
SELECT
[sJOB].[job_id] AS [JobID]
, [sJOB].[name] AS [JobName]
, [sJSTP].[step_uid] AS [StepID]
, [sJSTP].[step_id] AS [StepNo]
, [sJSTP].[step_name] AS [StepName]
, CASE [sJSTP].[subsystem]
WHEN 'ActiveScripting' THEN 'ActiveX Script'
WHEN 'CmdExec' THEN 'Operating system (CmdExec)'
WHEN 'PowerShell' THEN 'PowerShell'
WHEN 'Distribution' THEN 'Replication Distributor'
WHEN 'Merge' THEN 'Replication Merge'
WHEN 'QueueReader' THEN 'Replication Queue Reader'
WHEN 'Snapshot' THEN 'Replication Snapshot'
WHEN 'LogReader' THEN 'Replication Transaction-Log Reader'
WHEN 'ANALYSISCOMMAND' THEN 'SQL Server Analysis Services Command'
WHEN 'ANALYSISQUERY' THEN 'SQL Server Analysis Services Query'
WHEN 'SSIS' THEN 'SQL Server Integration Services Package'
WHEN 'TSQL' THEN 'Transact-SQL script (T-SQL)'
ELSE sJSTP.subsystem
END AS [StepType]
, [sPROX].[name] AS [RunAs]
, [sJSTP].[database_name] AS [Database]
, [sJSTP].[command] AS [ExecutableCommand]
, CASE [sJSTP].[on_success_action]
WHEN 1 THEN 'Quit the job reporting success'
WHEN 2 THEN 'Quit the job reporting failure'
WHEN 3 THEN 'Go to the next step'
WHEN 4 THEN 'Go to Step: '
+ QUOTENAME(CAST([sJSTP].[on_success_step_id] AS VARCHAR(3)))
+ ' '
+ [sOSSTP].[step_name]
END AS [OnSuccessAction]
, [sJSTP].[retry_attempts] AS [RetryAttempts]
, [sJSTP].[retry_interval] AS [RetryInterval (Minutes)]
, CASE [sJSTP].[on_fail_action]
WHEN 1 THEN 'Quit the job reporting success'
WHEN 2 THEN 'Quit the job reporting failure'
WHEN 3 THEN 'Go to the next step'
WHEN 4 THEN 'Go to Step: '
+ QUOTENAME(CAST([sJSTP].[on_fail_step_id] AS VARCHAR(3)))
+ ' '
+ [sOFSTP].[step_name]
END AS [OnFailureAction]
FROM
[msdb].[dbo].[sysjobsteps] AS [sJSTP]
INNER JOIN [msdb].[dbo].[sysjobs] AS [sJOB]
ON [sJSTP].[job_id] = [sJOB].[job_id]
LEFT JOIN [msdb].[dbo].[sysjobsteps] AS [sOSSTP]
ON [sJSTP].[job_id] = [sOSSTP].[job_id]
AND [sJSTP].[on_success_step_id] = [sOSSTP].[step_id]
LEFT JOIN [msdb].[dbo].[sysjobsteps] AS [sOFSTP]
ON [sJSTP].[job_id] = [sOFSTP].[job_id]
AND [sJSTP].[on_fail_step_id] = [sOFSTP].[step_id]
LEFT JOIN [msdb].[dbo].[sysproxies] AS [sPROX]
ON [sJSTP].[proxy_id] = [sPROX].[proxy_id]
ORDER BY [JobName], [StepNo]
Now, you need to look into Executable command to see the exact configuration file being used in the SSIS execution and accordingly take action.
[ExecutableCommand]: The actual command which will be executed by the subsystem.