Rig2690

So I have an 03 3500 dually stock and very well maintained (vin c HO but. 47re wth)... I thought it was a 48re any clues guys ... I'm new to the diesel world but very mechanically inclined ..Ok so the other day my trans cooler (heater) on the engines block must've went bad. So I did a flush and bypassed it on the side of the highway ��. Ran about 10 gallons of fluid through the transmission but couldn't find a filter. Well after the coolant flush she was running great. Well again the other day she started acting up. Would go into gear then act like it was in neutral. So I got real nervous then was towed to my shop then had to drive my work truck home......**** ford lol. Today I dropped the pan and the filter was clogged as all heck . I changed it and pumped the rest of the fluid out. Well she running Great now but should I be worried there was no metal shavings or chunks at all just kinda gooey on the magnet??? Any insight would help .
Thanks for the help everyone.