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:( At this point, I think your decision is where you would prefer to be stranded, San Salvador or Bogota.
Given your description, seems Bogota would be best since it is possible you can make the Santa Marta flight, especially if it's delayed as well and at least Bogota is closer to Santa Marta.
You can also ask for different routings.
For the future, if you don't like what one Agent is saying, call back.
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This is unfortunately standard practice in the industry. Delays are usually not acknowledged until the last minute and the sometimes hope that they will get shorter, so they don't want to tell people to not show up until much later, just in case. In very few cases I've managed to ge the airline to change my route to something better free of charge but that is less hand a handful of times.
What you should do now is follow the route they gave you. If you make the connection, great. If not, they will reroute you again. Depending on how late you arrive compared to the original plan, you may get compensation but only after you arrived, had time to file a claim and hear back. This takes long, just last month I got compensation for a situation where I was rerouted on flights that arrived over 24h after my original arrival date.
Given the delay, some credit cards offer some insurance, if you have bought the tickets with such a card but that really depends. If you do have one, it's time to read the fine-print to see if some coverage applies to your situation.