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Over the last three years, the San Francisco 49ers have had one of the most dominant defenses in the NFL. In 2011, defensive coordinator Vic Fangio guided the fourth-best defense in the NFL. In 2012, he coached the No. 3-ranked unit. And in 2013, he instructed the fifth-best defense.

Yet the past successes of San Francisco’s defense doesn’t necessarily mean it will find guaranteed prosperity in 2014. Why? Because right now, the 49ers are doing little to quell concerns about their retooled, injured defense.

Obviously, we are still very early into the preseason process, but some of the problems that showed up in San Francisco’s first preseason game against the Baltimore Ravens showed up again versus the Denver Broncos.

For a case in point, take a look at how badly the 49ers have been outscored through the first eight quarters of preseason play. Even though it is only exhibition play, there’s no reason as to why head coach Jim Harbaugh’s club should be outscored 57-3.

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The 49ers, especially on the defensive side of the ball, have a ton of talent at particular positions. Yet it’s evident that injuries and a looming suspension have taken a toll on Fangio’s unit.

Inside linebacker NaVorro Bowman is slated to miss significant time as he continues to recover from a torn ACL. Safety Antoine Bethea left Sunday’s game with a concussion. Outside linebacker Aldon Smith is expected to miss six to eight games for a series of off-the-field incidents, according to Matt Maiocco of CSNBayArea.com.

Defensive end Justin Smith is trying to bounce back from offseason shoulder surgery. And fellow defensive end Ray McDonald is trying to do the same after he had surgery for a torn biceps.

For a defense that has finished near the top of the league under Fangio’s watch, it’s hard to overcome the loss of prominent players at key positions. However, the good news is that Bethea, McDonald and Justin Smith should all be ready to go by the time the regular-season opener rolls around in September.

The bad news is that losing Bowman and Aldon Smith may be too much to overcome early on in the year. Does that mean the 49ers defense will immediately become obsolete? No, but it does mean we may end up seeing a defense that has more questions than answers.

Think about it: During the offseason, San Francisco not only lost safety Donte Whitner, it also lost cornerbacks Carlos Rogers and Tarell Brown. On the surface, Rogers and Brown may have not been All-Pro-caliber players, but they did have talent. Not to mention, they both knew Fangio’s system extremely well.

Sure, it may have been time to move on from both players due to old age and health, yet it’s clear from the first two weeks of the preseason that San Francisco didn’t do enough to replace Rogers and Brown.

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Yes, adding Jimmie Ward in the draft and Chris Cook in free agency were steps in the right direction, but it’s apparent that the 49ers secondary still has a long way to go before Week 1 of the regular season.

Moreover, when you add San Francisco’s secondary woes to its injury and suspension woes, it’s hard to feel confident about the 49ers defense as a whole.

As it stands, the defensive line, linebacking corps and secondary are all missing key players. Yet, as mentioned above, things will change once Justin Smith, McDonald and Bethea return from injury.

Nonetheless, after two embarrassing preseason performances, San Francisco has to go back to the drawing board defensively. It has to figure out which reserve players can step up and fill in effectively until its core starters return.

With the way things have gone for the 49ers defense so far, that may end up being easier said than done. It may also end up being a process that lingers on into the early stages of regular-season play.

Fortunately for the 49ers, they have one of the best head coaches and defensive coaching staffs in the game. And that’s not even a question considering how well they have performed during Harbaugh’s tenure in the Bay Area.

Yet it’s safe to say that San Francisco has some work to do.

But isn’t that what preseason play is for? In this time before the regular season, teams dedicate their resources to identifying their weaknesses and assembling the best 53-man roster possible.

Despite the fact the 49ers have done Little to quell concerns about their retooled, injured defense, they will find a way to overcome adversity and compete at a high level. They always do.

The only difference is they will need to work a little bit harder to do so. Furthermore, quarterback Colin Kaepernick and the 49ers offense will also have to aid Fangio’s defense until Bowman and Aldon Smith return to the starting lineup.