xlsgen 4.9.0.4 adds a new property to the xlsgen object model, to be used before loading files. This Style optimisation property allows to disable the style optimisation algorithm done by xlsgen on behalf of the client application, trying to remove useless styles. This algorithm is on by default and has been going on for years, it is nothing new. By setting this property as false, the algorithm is disabled, in order to meet scenarios where style optimization is not expected to occur (i.e. pure template scenarios).
engine.Workbooks.StyleOptimisation = False
engine.Open("mytemplatefile.xlsx", "")
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