The CSV Import extension does support importing more than one CSV file. I personally have dozens of real world CSV files which have 10’s of thousands of combined rows supplied by other users which I use for testing the extension.
I suspect on the second import the Entry ID column was mapped and those values in CSV files in that column matched the entry ID assigned by the WordPress database when inserting the first CSV file. When matching entry IDs are found, the existing in entry is updated rather than a new entry being inserted. If that is the case, that could explain why entries appears to have been lost and photos being associated to the second import entries. I say appears because the CSV Import can not delete entries and the CSV import process does not work with images at all. Unfortunately there is no automatic way to revert changes, unless, you happen to have a db backup that you can restore.
If you can attach both CSV files, I can take a look and confirm my guess.