There are various differences mentioned by rail fans and no mention of it is made in any publicly accessible IR documents.
Some say that the 'E' suffix was given to indicate that the loco is air-braked. Another possible difference is in the location of the Dynamic braking resistors, which were bottom mounted in the initial models and then moved to the top of loco (these locos apparently got the 'E' suffix, but now all WAP-4 locos have the DBR opening out on the roof of the loco). Whatever the difference might be, it is only a minor difference in construction and not any major difference in speed/performance.
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more... As to why only BRC shed holds these locos, many loco sheds have their own naming conventions. Some tend to be very specific about the loco's specs, while others follow different conventions. For example, some sheds label WAP7 with IGBT converters as WAP7-i, while other sheds do not have the 'i' suffix. Similarly, with the WAM4, WAG5 class locos, there are many complicated loco names that each shed follows ( WAM4/6PE, WAM4+DB+HS etc). The loco's name in this case, is just based on the shed's convention.