What was the reason behind it.?
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From the text:
They bury their dead with their heads directly downward, because they hold an opinion, that in eleven thousand moons they are all to rise again; in which period the earth (which they conceive to be flat) will turn upside down, and by this means they shall, at their resurrection, be found ready standing on their feet. The learned among them confess the absurdity of this doctrine; but the practice still continues, in compliance to the vulgar.
Lilliputians used to bury body of dead people upside down as they had a belif that after a millions of years the earth would also turn upside down, resulting in making the people alive once again and the people who are alive as dead. They were following this ritual since a long time and they also believed that whatever their ancestors used to do was surely appropriate and they should also follow the same rituals ahead. They also believed in not modernising their views and thoughts and continuing with the same old and ancestorial thoughts as they were all deeply connected to their ancestors and believed that if they did a particular thing that is the first and last word said on that particular topic and no one had right to change or offend that ritual in any way. They were forced to follow the rituals whether they liked it or not.
Gulliver's Travels from where the question is been extracted.