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I don't agree that a short year means $0 income because it is earned on 12/31. There is P&L for that period. If for some reason instead of a short plan year the owner had a short tax year, there would be income for the short period. It is just unknown without going through all the calculations. My two cents

It's a per filing fee and your filing is supposed to correct all errors, so 2018 and 2019 all together. You/they should also review thoroughly for any other issues that may need correction and include as well.

A little late to the game here but I agree that filing them as soon as you learn of error is the best course of action. It is likely that you will receive a Notice 972CG after you file the Forms 1094-C and 1095-C late. As Brian stated above, there is a way for employers to dispute the proposed penalties in a Notice 972CG. An employer should frame its response using the Treasury Regulations at 301.6724-1. I have had a lot of success completely abating the penalty for clients although the IRS may be more stringent moving forward. Each case is very fact specific. I wrote an article that explains the Notice 972CG that may be informative - https://accord-aca.com/articles/notice-972cg . Please don't hesitate to reach out if you need assistance.