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I don't think the issue has to do with the import across game versions. The changes to focus on were the 1969/1970 thing and that maybe the "all teams to controlled by me" is conflicting with brining players in. Is this the first season that you are on 26? If it is you can backup the 25 version of the game under a different name, load it, reimport the game under that different name into 26 and not change the year... and then compare. So, I'd try and isolate that variable.
If you want to start investigating the game already in 26 first, first thing I'd do is backup the game since if the next steps solve something, you'll want to go back to that restoration point.
Then I'd take off the "all-teams-controlled-by-me" and try reimporting them. Or advancing a day with it off and see if they show up. Since you know when they first played a game from baseball-reference, I might advance to that day and see if the real lineup forces them into the game.
So, variations like that to test what did it and isolate the issue would be my approach.
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