Yeah, put back as original. Maybe cut a new sheet if you can identify pinholes in it, that's about it.
1. the yellow film is Dupont Kapton (Tm) https://www.dupont.com/products/kapton-mt.html
very high temp rating, fine voltage rating.
Specifically designed for high thermal conductivity. Bergquist Sil pads, mica, etc may not be as thermally conductive or resistant to puncture.
Hmm, I'm not aware that there's anything they can (or do) do, to affect the thermal conductivity. It's actually a rather pitiful material in that respect, that is, it's a rather good insulator both electrically and thermally. It's just such a good dielectric that a very thin layer will do -- which makes it usable, if still unimpressive. To be clear, not that it's terrible, there are certainly plastics with lower conductivity; but it's also a long ways away from, say, alumina or graphite.
Mica is the same way, terrible conductor thru-plane but can be cleaved very thin so it does alright.
By "unimpressive", I mean on the order of 0.5-2 K/W added thermal resistance (RthC-HS), depending on film thickness and package size. Typically the heatsink is the limiting factor anyway, so it's not a big deal. (The heatsink here looks like it's going to be more like 2 K/W overall, and say we divide that by however many devices are on it, that's still not much above the 0.5-2 range. So you are right to guess, thermal performance could be improved perceptibly here, with improved materials.)
There are better materials these days, with conductivity 6 W/(m*K) and higher -- compare with classic (firm rubber, usually gray) Sil-Pads(TM?) in the 0.5 range (I think?) -- but beware they are also much, much softer. And usually thicker. A different clamping strategy is needed -- and especially for components that were positioned for a ~0.5 mil film, they're going to be in all the wrong place once you get 20 mils or more in there.
There are also self-adhesive and phase-change kinds; these stick in place better, and are stiffer (or, are once melted in place), so might be better replacements for Sil-Pads as such. But again, I wouldn't recommend replacing film with either kind, for the above reasons.
Edit: Ahh, fascinating. Kapton(R) HN I guess is the "default" kind, and says 0.2 W/(m*K). Or "FPC" at 0.12. The linked MT type is a whopping 0.46 -- they do indeed do something with it! And in a thin layer, indeed that isn't bad at all. Take a typical TO-220 at 10x15mm, a 0.025mm layer is 0.36 K/W. Add a little (~0.1 K/W?) for grease and you aren't much higher than the package itself (TO-220s are often in the RthJC ~ 0.3 to 2 K/W ballpark).
Tim