The problem that I can see with using a flexible pipe is that you may not be able to ensure a continuous fall along the length of pipe and so end up with an air lock.
In principal, provided that it is made of a suitable material and is the required size for the location of the pipe, then I cannot see that you cannot use it but it may give you more headaches than you have cured... whats wrong with using rigid pipe?
Why, what height is boiler from floor. you will have a drop on it for most off the way even bit of horizontal is ok , Water will get out without backing up into the boiler.
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