As to the second property, it sounds like both the plumbing work and the subfloor constitute "improvements". The cost would be added to the property as a new "asset" and depreciated separately over 27.5 years (you should be in about year 6 or 7 on the main property).
There are some articles here to start with.
https://www.nolo.com/legal-encyclopedia/repairs-vs-improvements-how-tax-deductions-differ-landlords....
https://www.dbbllc.com/newsletters/focus-our-tax-e-newsletter/irs-clarifies-capital-improvement-vs-r...
It can get complicated if you are trying to optimize your tax position. Sometimes, it would be helpful to take the entire cost as a repair (expense it all at once to generate a large loss) rather than depreciating it. The IRS has some regulations on that. There are one or two "safe harbors" that allow you to expense improvements even if they would normally be depreciated. I'm not familiar enough with those rules to quote them, @Anonymous_ might know or you can look them up or consult a tax professional. But if this work does not fit into the safe harbor, you probably need to depreciate it rather than expense it.
And this does not fix the "placed in service" problem with the first property, unfortunately. As far as "what were we supposed to do?", you take it on the chin like everyone else. I don't get to deduct the cost of replacing the leaking service water line on my house, because it is personal property. It's just maintenance and repairs I have to pay as a homeowner. If you are running a business (including rental property), you can deduct costs against income, on the theory that you should only pay tax on the net profit after expenses and not the entire gross proceeds. But there has to be some line you cross between personal use and business use, and the IRS draws that line at "placed in service."
