I figured it out. This is the answer from the manual:
*Debugging external assemblies
When debugging external assemblies, both the assembly file and a .pdb-file with symbolic information are required. Only assemblies with loaded .pbd files can be debugged. As pbd-files are rather large, it is better to disable loading symbolic information in the working project.
Registry keys that control the loading of symbolic information
You can use the following registry keys to specify whether .pdb-files should be loaded:
HKEY_CURRENT_USER\Software\ABBYY\FlexiCapture\11.0\Controller\ScriptSupport\ [LoadSymbolsFromOriginalPath] - specifies whether to load pdb-files from the original folders of the assembly files (set the key value to "true" to load .pdb-files);
HKEY_CURRENT_USER\Software\ABBYY\FlexiCapture\11.0\Controller\ScriptSupport\ [PDBSearchLocations] = <path to="" the="" folder="" with="" pdb-files=""> - sets the search paths for .pbd-files (paths must be listed separated by semicolons; the search result is a .pdb-file with symbolic information whose name coincides with an assembly name).
These keys are not created in the registry by default. If required, the administrator may add these keys into the registry of the user's operating system.
For the changes in the registry to take effect, you need to restart the program.
For debugging an assembly, connection to managed code must be used.*