This is the first time I encounter such issue. This is certainly not the expected behaviour. Are there any errors in the upgrade log concerning a problem with the ecommerce module?
I suppose the tools can be removed when the module is not installed which is done when the license doesn`t support ecommerce, however this was not the case.
I have tested upgrading from 3.7.1885 to 4.4.2117 and didn`t encounter a problem, the ecommerce section in the page toolbox was present.
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