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Engines can certainly be salvaged, depending on how much damage has been done. Oil gets filtered slightly at the suction screen in the sump, then better as it passes through the filter. Cut the filter open (use a filter cutter, looks like a big pipe cutter with sharp wheels), and lay the paper media out flat under a good light. You'll get an idea how much metal is in there. I'm not suggesting that serious oil shavings don't deserve a full disassembly and cleaning of block and heads to get shavings out. But a relatively easy rod bearing noise may not demand that. Again, depending on the amount of metal loose in the system.

Reminders: Rod bearings fail before main bearings, thanks to the way oil flows through the crankshaft. Our engines don't have hydraulic lifters, so don't suffer from some of the oil-flow afflictions that hydraulic-lifter engines might with dirty/contaminated oil. We do have engine-oil hydraulic actuators for VCM in the cam boxes, though, that are very sensitive to particle-contaminated oil. You can remove rod bearing caps and inspect individual rod bearings one at a time after removing the oil sump. Look for metal particles in the cam boxes after removing the intake plenum and the cam covers. Check the valve clearances. These first steps are targeted at identifying the source of the noise and the metal found in the sump.
I seem to remember hearing some engine builders look at the VTEC solenoid screen, if they see metal there they know the engine has been run low or too long and is toast.
 
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Engines can certainly be salvaged, depending on how much damage has been done. Oil gets filtered slightly at the suction screen in the sump, then better as it passes through the filter. Cut the filter open (use a filter cutter, looks like a big pipe cutter with sharp wheels), and lay the paper media out flat under a good light. You'll get an idea how much metal is in there. I'm not suggesting that serious oil shavings don't deserve a full disassembly and cleaning of block and heads to get shavings out. But a relatively easy rod bearing noise may not demand that. Again, depending on the amount of metal loose in the system.

Reminders: Rod bearings fail before main bearings, thanks to the way oil flows through the crankshaft. Our engines don't have hydraulic lifters, so don't suffer from some of the oil-flow afflictions that hydraulic-lifter engines might with dirty/contaminated oil. We do have engine-oil hydraulic actuators for VCM in the cam boxes, though, that are very sensitive to particle-contaminated oil. You can remove rod bearing caps and inspect individual rod bearings one at a time after removing the oil sump. Look for metal particles in the cam boxes after removing the intake plenum and the cam covers. Check the valve clearances. These first steps are targeted at identifying the source of the noise and the metal found in the sump.
This is all true but at current mechanical labor rates you could wind up putting a lot of time and money to a motor that is already dead. But let me ask the original poster this, since you raise a good point and there is obviously no downside to getting more information to make a better decision: is the shop that made the diagnosis good and do they know Hondas? We are all sitting here from afar but they may have said more, or the engine noise may be telling. Also, it may not be that much additional labor to drop the oil pan and see what the bottom end looks like.
 
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