You either don't import new private keys... or you don't run in pruned mode. Attempting to do both is going to cause issues.

If you import to a pruned wallet, you will need to either rescan (which will require redownloading and reprocessing the entire blockchain) or accept that your wallet may not show an accurate transaction history/balance for that particular address or addresses.

If you think you're going to be importing private keys often (multiple times), get more storage and don't run pruned... or use a different wallet like Electrum that will allow you to import keys without storage/rescan penalty.