You shoul read the program help file! 😀
“execute one query” and “execute all queries” are about queries in the Query pane (a Query Tab as of SQLyog 4.2). Here queries are delimited with the ; (semicolon) delimiter.
“execute one query” executes the query where the cursor is positioned.
“execute all queries” executes all queries on the active tab,
It has nothing to do with queries saved to disk! Only queries that are loaded into the Query pane.