Yes there are issues with syncing to exchanges, although in most cases this is down to the exchange and not Koinly. E.g. Binance’s Convert function doesn’t sync to Koinly because Binance doesn’t publish it on the API.
However Koinly handles conversion just fine. For a manual convert transaction you use “Add Transaction > Trade”.
For syncs to the blockchain e.g. ERC20 tokens, and most centralised exchanges, they usually work correctly. Sometimes for reasons I haven’t fully worked out, conversion transactions sync as a Sell into fiat followed by a Buy. In these cases, if you want you can select both transactions and an option to merge them appears at the bottom of the screen.
A lot of the confusion on these boards comes from overloading of terms “trade”, “exchange”, “swap” etc between Koinly and other sources. Koinly’s help does a good job of explaining what they mean by all these terms.