Lynch and the 49ers selected Thomas with the No. 3 overall pick in 2017. Twenty-eight picks later, they selected linebacker Reuben Foster. Ninety selections after that, San Francisco drafted running back Joe Williams.
Two years have passed, and neither Foster nor Williams is on the 49ers roster. Foster because of off-the-field issues and Williams because of an inability to get onto the field.
Foster and Williams represent two instances in Lynch's and Shanahan's first draft where the duo took risks, and they didn't work out.
The 49ers have just six selections in the upcoming draft. That's three fewer than the team ended up with in 2017 and four fewer than last year.
"We're used to having more," Lynch told reporters on Monday. "It's uncomfortable just by virtue of that, what we're accustomed to."
The 49ers would love to add to this year's count but know if that doesn't happen, they have to make each pick count. Taking risks in the draft may be a luxury the team can no longer afford.
The 49ers' pre-draft evaluation process has evolved over the past two years to limit the potential risks of making another costly mistake.
"There's certain tweaks we've made," Lynch explained. "Our 30 visits this year, we brought people more in a group setting. We want to see how they interact with other people. So, those are subtle things that we do. But, there's so much that just goes into the research of these players. You learn something every year.
"I think the most important thing, you impart upon your scouts, upon your staff is, 'We have to be as thorough as humanly possible.' Anything we can learn about these guys is valuable information.
"I'm real proud of the work we've done with our staff to get as much information to be equipped to make as good a decision as possible."
The Foster and Williams situations provided valuable lessons for Lynch and Shanahan.
"If you aren't always learning, shame on you, shame on us," Lynch said. "I think with Reuben; I think we somewhat accounted for it by where we drafted him. I think we had him at a certain value. We didn't draft him there. That doesn't excuse us. It's a shame."
Drafting Foster in 2017 proved to be a costly mistake. Literally costly to the tune of $54 million. That's the salary linebacker Kwon Alexander, who was brought in to replace Foster, could earn over his new four-year deal with the 49ers.
"We're very happy to have Kwon Alexander, but that came at a heavy price," Lynch continued. "We would've much preferred to have Reuben still playing here. So, of course you learn a lesson. If you don't, like I said, shame on you. You work hard to try to identify what is the lesson that you learned. We know in-house what those lessons are.
"As to Joe, I think that was a pick, it didn't work out. But, in every scenario, whether something worked or didn't work, you take note. We try to do that in each individual case."
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