I have 2 tables in which I want more robustness and fortunately don't require frequent rapid fulls of data and examination. All other tables would inevitably be MyISAM.
Can I safely use both (I've read a handful of discouragements from this) without fearing bugs or data getting affected by differences between engines?
You CAN but this introduces a number of disadvantages:
So basically, I'd encourage you to switch wholly to InnoDB. Then you can pretty much forget about MyISAM and not devote resources to it, and get the full benefits of using InnoDB. Anyone who thinks MyISAM is faster is either not tuning InnoDB correctly, or has such small data that who cares.
MyISAM does faster table scans, but if you're doing those on large tables, you have bigger problems.
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