The government's move to protect uninsured deposits at Silicon Valley Bank was a relief for many company founders, but the bank's demise likely will leave a trail of challenges for startups, including making cash to fund growth a little harder to come by.

"The most important thing is it seems like payroll is going to hit on time, but there are still plenty of things to be concerned about," said Healy Jones, vice president of financial strategy at startup-focused accounting firm Kruze Consulting, which counts nearly 800 venture-backed startups as clients.

Though the government guaranteed all deposits at SVB, including those above the Federal Deposit Insurance Corp.'s $250,000 limit, it remains unclear whether companies will be able to draw on funds from venture debt loans. SVB touted itself as the first bank to offer such loans, which startups use to give themselves breathing room before they need more funding from investors.