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The best way to side step this issue (aside from increasing carry cap), just pick up the many items (like monster parts or skill drops like lumber/ore/etc), or the other ones (rare drops, potions, food and whatnot that doesn't come in near countless numbers), after another. Since you said you put them in storage in quick ref I guess you have the dedotated ram companion. Because if that is not the case and you would be using the talent that puts stuff in the storage, it would erase everything else that still lies on the floor. That used to be the only way to get things out of your pockets before the companions, it makes kinda sense to a degree that a good bonus is having a downside. But at some point it's just irrelevant.
These days I often farm exactly my max carry cap of logs and there's nothing left afterwords. At least no logs left to pick up.
I do think there may be a bug in the code somewhere but I'm not sure.
Example using OPs numbers: When you come back from AFK to 50k+ Tropilogs, it drops two stacks of 25k+ Tropilogs. I don't know the capacity of your log stacks, so I'll just use 10k for this example. Let's say that you have three inventory spaces available. When you pick up the first stack of 25k+ Tropilogs, you have two spaces of 10k Tropilogs and another space of 5k+ Tropilogs. If you pick up the second 25k+ Tropilogs stack, it will fill the 5k+ stack up to 10k and delete the rest. If you get rid of that 5k+ stack (drop it or quick ref stash it) so you don't have a partial stack before trying to pick up the second 25k+ stack, then you will fill that empty third space with 10k Tropilogs and the remaining 15k+ Tropilogs on the ground will stay there and not get deleted.
I don't know why, but the deleted items all comes down to having a partial stack in your inventory when you try to pick up more than you can carry. The fact that AFK drops are split into two stacks when they drop just increases the chance the first stack will give you a partial stack when you try picking up the second stack.
If you know that there is more than you can carry, you just need to be careful to make sure you don't have a partial stack if you want to prevent the game from deleting the extra items you can't carry.