You may need to update documents inside your FlexiCapture training batches to the latest version of  Document Definition. The simplest way is via Project Setup station GUI (right-click on batch > Update to the latest version). Below is the example of updating via FlexiCapture Web API

Step-by-step guide

The idea is that update requires documents to be re-recognized using the current version of Document Definition.

The original project with API usage example: https://help.abbyy.com/en-us/flexicapture/12/developer/unattendedexample

Project name - Program.cs:105

Adjust the project with the following code

if (project.Name != "eui") continue;

private static void Update(FlexiCapture.
        FlexiCaptureWebServiceSoapClient service, int userId, int sessionId, int projectId, string filename)
        {
            //findU
            var uid = service.FindUser("ABBYYUKR\\NShevchenko");
            FlexiCapture.User user;
            service.GetUser(uid, out user);

            var listst = service.GetAvailableTasks(sessionId, projectId, 500, false);
            service.GetTaskInfo(0);

            var batches = service.GetBatches(projectId,sessionId,false);
            for (int i=0;i<batches.Count;i++) {
                FlexiCapture.Batch b = batches[i];
                service.ProcessBatch(sessionId, b.Id);
            }

If the server is not local, then you should configure the reference.
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More information about API usage: https://help.abbyy.com/en-us/flexicapture/12/developer/api