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Even if the cooler lines had air in them, it won't be circulating in the system long because when it travels into the transmission oil pan it simply floats up and eventually out the vent on top of the transmission. There is always air in the transmission it just doesn't tend to circulate through and even if it does unless it's a large amount (which means your fluid is low) it won't cause problems. My advice is check your fluid level while the vehicle is warm, running, and in park. Also, you may have lost a lot of fluid from the line that I'm assuming broke or was leaking and overheated the transmission.

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Q: Can replacing a transmission cooler line cause air to get into the system and cause slippage and poor gear shifting in an automatic transmission?
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