Well, I'm not sure there is really a question in there but I'd suggest that you aren't out any $ unless he withholds your security deposit or sues you for the cost. Without a final walk through and with the long history of leakage, I'd say he'd have a hard time proving that it was your fault... even with a missing piece.
If he damages you, I'd suggest contacting an attorney in your area.
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Well, it's a bit more dire than that. It sounds like there is serious leakage in the downstairs unit and that could result in anything from the tenant's annoyance to serious water damage/mold/etc. The downstairs unit may sue the landlord. Assuming he has insurance, they will handle the claim. From what you're saying I doubt any lawyer would seriously think they could transfer liability to you. So, in all likelihood, not much to worry about.
Of course if LL uses this as an excuse to withhold your deposit you're probably in the right to reclaim.
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