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Will adding blocks in the middle of a chain cause any problems with the block order for Abe?
I know of one, possibly two bugs affecting this situation. First, Abe sometimes crashes by exceeding Python's recursion limit when rescanning. This does not produce wrong data, and I work around it by deleting rows from chain_candidate, updating chain.chain_last_block_id, and retrying.
I have noticed slight deviations in statistical values like Coin Days Destroyed from one Abe instance to another. (The values on the homepage depend on server system time, but on a given block's page they should be identical.) I suspect rescanning may create statistical discrepancies. The ones I've seen were slight (under 1%).
I do not know of any bugs affecting address balances, transaction links, etc. But I can offer no guarantee.