CLI ignoring dataset(s) in the reported issues

It appears that the core engine (CLI) is disregarding file(s) encountered on a list of files with different filenames if they have the same top level properties used for identifying different datasets. Example: I made a copy of a lb.json as lb1.json and adjusted only properties for a column on the lb1.json file. The rest of the file untouched. The output I get indicates the 2 files in the dataset details (lb.json and lb1.json); however, the reported issues are only for lb1.json.

The source json files can be found at:
[examples/sdtm](https://github.com/cdisc-org/DataExchange-DatasetJson/tree/master/examples/sdtm)
and
[lb1.json](https://github.com/user-attachments/files/21417140/lb1.json)

The revised lb1.json file only contains the following difference against the lb.json file:

XLS Output:

[core_val_data_examples_api_sdtm.xlsx](https://github.com/user-attachments/files/21417264/core_val_data_examples_api_sdtm.xlsx)

Reproduce the report with the CLI using the files in examples/sdtm and the supplied lb1.json, comparing it with lb.json. Inspect how the CLI associates files with datasets and selects files for reported issues. Done means the output reports issues from both lb.json and lb1.json when their relevant contents differ.

Written by the indexing model from the issue text.