The identify of an object is a choice, a way of looking at it. The "right" way of making this choice is the way that best achieves your values.
I think that's really the central point. The metaphysical principles which either allow or deny the "intrinsic philosophical risk" mentioned in the OP are not like theorems or natural laws, which we might hope some day to corroborate or refute - they're more like definitions that a person either adopts or does not.
I don't see either as irrational
I have to part company here - I think it is irrational to attach 'terminal value' to your biological substrate (likewise paperclips), though it's difficult to explain exactly why. Terminal values are inherently irrational, but valuing the continuance of your thought patterns is likely to be instrumentally rational for almost any set of terminal values, whereas placing extra value on your biological substrate seems like it could only make sense as a terminal value (except in a highly artificial setting e.g. Dr Evil has vowed to do something evil unless you preserve your substrate).
Of course this raises the question of why the deferred irrationality of preserving one's thoughts in order to do X is better than the immediate irrationality of preserving one's substrate for its own sake. At this point I don't have an answer.
The metaphysical principles which either allow or deny the "intrinsic philosophical risk" mentioned in the OP are not like theorems or natural laws, which we might hope some day to corroborate or refute - they're more like definitions that a person either adopts or does not.
What do the definitions do?
A new paper has gone up in the November 2011 JET: "Ray Kurzweil and Uploading: Just Say No!" (videos) by Nick Agar (Wikipedia); abstract:
The argument is a variant of Pascal's wager he calls Searle's wager. As far as I can tell, the paper contains mostly ideas he has already written on in his book; from Michael Hauskeller's review of Agar's Humanity's End: Why We Should Reject Radical Enhancement
John Danaher (User:JohnD) examines the wager, as expressed in the book, further in 2 blog posts:
After laying out what seems to be Agar's argument, Danaher constructs the game-theoretic tree and continues the criticism above:
One point is worth noting: the asymmetry of uploading with cryonics is deliberate. There is nothing in cryonics which renders it different from Searle's wager with 'destructive uploading', because one can always commit suicide and then be cryopreserved (symmetrical with committing suicide and then being destructively scanned / committing suicide by being destructively scanned). The asymmetry exists as a matter of policy: the cryonics organizations refuse to take suicides.
Overall, I agree with the 2 quoted people; there is a small intrinsic philosophical risk to uploading as well as the obvious practical risk that it won't work, and this means uploading does not strictly dominate life-extension or other actions. But this is not a controversial point and has already in practice been embraced by cryonicists in their analogous way (and we can expect any uploading to be either non-destructive or post-mortem), and to the extent that Agar thinks that this is a large or overwhelming disadvantage for uploading ("It is unlikely to be rational to make an electronic copy of yourself and destroy your original biological brain and body."), he is incorrect.