If this is still an issue try changing the server and if that doesn't work recover from seed...
exactly this, thanks for your contribution, i had the same issue as OP and switching server was enough to recover that pruned transaction. 
Topic: Funds disappeared from electrum. "pruned transaction outputs" (Read 1191 times)
If this is still an issue try changing the server and if that doesn't work recover from seed...
It is the total amount you've spent with your Electrum wallet before the latest transactions that the current server you're using serves you.
No idea what's happened here. Didn't update or anything. Just started up electrum and was -2.87 BTC in the history.
Any ideas.
I am pretty worried.
Any ideas.
I am pretty worried.
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