I have a 200 v 2.5 amp brushed dc motor that the field magnets had parted ways with the housing!
I will disassemble the motor and remove the magnets(they are JB welded in)
To recap: Your magnets came loose "Parted ways within the housing". You JB Welded them back in but you're unsure of the proper orientation. If they are not properly oriented then yes, you have to remove them WITHOUT BREAKING THEM. I don't know how strong the JB Weld is.No need to remove any magnets.
I've had magnets break apart. When I tried to put them back together at the fracture they resisted going back together. Now; I don't know this for sure, but if two "South" magnets are attempted to be put back together I would imagine they would resist each other. If you put a "North" and a "South" together to make a longer magnet then that may be the issue. I'm talking about things WAY over my head. Remember, a North magnet end and a South magnet end will attract whereas two norths or two souths would repel. But you know that much about magnets. Your magnets are not designed with one longitudinal end North and the opposite end South. Rather, the clam shell of the magnets are magnetized to where you're looking at the end of the magnet and on one side of the C the north is pointed at the center of the housing while the south end is pointed outward. The other side of the housing is just the opposite.
EDIT: Like this

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