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This should not be happening, as Backdrop now automatically enables Entity Plus when upgrading (provided the Backdrop module is present in the upgraded site's modules folder).
I've found instances where this happened, and those were usually due to code problems; for example, having a class that extends an E+ class in a file shared by other functions that are loaded early in the upgrade process (e.g. hook_views_data()).
The only way to find out what the problem is is to step debug the upgrade process. Typically these issues can be fixed relatively easily.
OK, I took a quick look. There are a few spots where Entity Plus is needed before it's enabled in the upgrade process. Some of these could be fixed, but I agree that it's simpler to enable the stub module in the D7 site before upgrading.
Workaround is to enable an Entity Plus stub module on D7, or temporarily disable this module to get through the upgrade.
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