It sounds like there are many rows with IdStop > 500 and there is not good index to solve the query, so SQLite has to scan the entire table and check if the condition IdStop <= 500 is met. I guess the scan order is similar to IdStop order, therefore after IdStop = 500 is reached, a lot of rows remain to be scanned but none of them meet the condition, that is the reason why you observe that delay, SQLite is scanning the rest of rows.
To solve the problen you need to find a good index. Probably an index with IdStop as the first column in the key and IdCp as the second, will work. You should also experiment with JOIN order. Generally, placing the smaller table first is faster.