Updated to reflect closing share prices and additional analyst commentary NEW YORK ( TheStreet) -- Linn Energy ( LINE) filed an amended S-4 with the Securities and Exchange Commission that moves the company forward on its acquisition of Berry Petroleum ( BRY), but leaves open some issues that have plagued the embattled oil and gas driller in recent months. Linn Energy said in its amended S-4 filing that the ratio of its proposed all-stock acquisition of Berry Petroleum remains unchanged. The company also said it re-defined some non-GAAP financial metrics such as maintenance capital expenditure and distributable cash flow (DCF). However, those changing definitions don't appear to have impacted Linn's underlying financial picture. The company continues to offer Berry Petroleum investors 1.25 shares of LinnCo ( LNCO) for each of their shares. Meanwhile, Linn Energy abandoned reference to "maintenance capital expenditure" and now uses the term "discretionary reductions for a portion of oil and natural gas development costs." This metric includes estimated drilling and development costs to convert the company's energy reserves to producing status. The metric doesn't include the historical cost of the company's acquired oil and gas properties. Overall, Linn Energy reported about $112 million in discretionary reductions for a portion of oil and natural gas development costs, the same figure the firm reported for its maintenance capital expenditure in previous disclosures. Linn Energy's decision to eliminate DCF also had no impact on the firm's non-GAAP financial information. The company continues to report that it paid out $38.5 million in dividends to shareholders in excess of its cash flow from operations. Linn Energy finances any shortfall of operating cash flow relative to dividends paid to shareholders with debt. While Linn Energy was able to provide new information to investors about its non-GAAP accounting and the terms of its proposed acquisition of Berry Petroleum as a Sept. 30 record date nears, the company didn't have new information about the SEC's informal inquiry into the firm, which was disclosed in July. "LINN and LinnCo are unable to predict the timing or outcome of the SEC inquiry or estimate the nature or amount of any possible sanction or enforcement action the SEC could seek to impose, which could include fines, penalties, damages, sanctions, administrative remedies and modifications to LinnCo and LINN's disclosure, accounting and business practices, including a prohibition on specific conduct or a potential restatement of LINN's or LinnCo's financial statements, any of which could be material," the company said. Taken as a whole, Linn Energy's disclosure puts to rest risk that the company's amended S-4 would alter its non-GAAP financial results, an outcome that might have raised new questions about the sustainability of the firm's finances. Still, the company made it clear to investors that its amended S-4 shouldn't be seen as material to informal regulatory inquiries. "The SEC inquiry may continue after the effectiveness of the registration statement," Linn Energy said. "This picture to me doesn't change the end result," Michael Peterson, a managing director of research at MLV & Co., said of Linn Energy's amended filing. Peterson added in a telephone interview that he still expected Linn Energy and Berry Petroleum shareholders to approve the proposed merger given the dividend yielding characteristics of the combined company. "There is nothing here to suggest to me that Berry shareholders won't approve this transaction," Peterson said. Linn Energy's accounting practices and the non-GAAP metrics that drive its dividend have come under scrutiny in recent months from Barron's and independent research firm Hedgeye Risk Management. Both Barron's and Hedgeye argue Linn's use non-GAAP accounting figures overstates the cash flow it can pay out to shareholders and under-reports the expenses tied to its hedging practices and capital expenditure. Hedgeye also calculated that Linn Energy's cost of replacing its oil and gas production was about $25 per barrel of oil equivalent (BoE), while the company's financial results and analyst calculations generally indicate replacement costs of about $15 per BoE. If Linn Energy and Berry complete their merger, it would likely refute many of the concerns raised by Barron's and Hedgeye. The prospect the SEC approves Linn Energy's accounting disclosures could undermine analysis that the firm has not been upfront with its investors. A merger could also help Linn Energy increase its dividend payout to $3.05 a share, on an annualized basis, according to the company's projections. However, some analysts now speculate that Linn Energy might maintain its annualized dividend of $2.90 a share in order to improve its coverage ratio. Wells Fargo analyst Praneeth Satish said in a client note Wednesday that Linn Energy remains "far from being a done deal" and noted the prospect of a revised exchange ratio and shareholder resistance as lingering risks. Linn Energy may also now trade at a slight discount to peers due to reduced financial transparency, the analyst added in a reiteration of his 'hold' rating. Earlier in September, the company alerted investors it was "working diligently" to file its amended S-4. On Sept 12, Linn Energy said it would acquire Permian Basin drilling assets for $525 million, however, the company hasn't yet made a filing with the SEC about the acquisition. Linn Energy said it would finance the acquisition with proceeds from a committed $500 million senior secured term loan and borrowings under its revolving credit facility. The company did not disclose which lenders will be financing the transaction in its press release. In August, Linn Energy added to its credit facilities by $1 billion, increasing its total lenders to forty-one. Linn Energy shares fell over 3% in Wednesday trading to $26.97, cutting five-day gains to just over 11%. LinnCo shares were down a similar amount to $29.90. Berry Petroleum shares fell less than 2% to $44.14. The exchange ratio of Linn's proposed acquisition values Berry Petroleum at $46.2375. Jim Cramer, founder of TheStreet and contributor to Real Money Pro, currently owns Linn Energy shares in his Action Alerts PLUS charitable trust, along with co-portfolio manager Stephanie Link. Cramer has supported Linn Energy and invited CEO Ellis on his CNBC show Mad Money to rebut Barron's analysis. On July 2, Link said in a Real Money Propost that the charitable trust would sell 1,400 Linn Energy shares at $29 apiece given the SEC's informal review. Action Alerts PLUS continues to own 1,000 Linn Energy shares after its stake sale, roughly 1.2% of the overall portfolio.