The two companies have also swapped a total £315m debt they owed to Sir Tom for shares.
The swaps leave Sir Tom's private equity business with big shareholdings in ventures which have only around £50m net assets between them.
However, Sir Tom said the transactions leave the retail and property investment groups free of debt and in good shape to return to the acquisition trail.
He said: "These actions are at the high end of prudence but put us in a position to both continue to invest in our current portfolio... and to seek acquisitions which fit with our portfolio and opportunity for growth."
The challenges Sir Tom has faced in the retail and property investment businesses are writ large in the latest filings by the West Coast Capital Holdings and Trading ventures.
These were used by Sir Tom's West Coast Capital private equity arm to place huge bets on both sectors.
After making around £290m from the sale of his Sports Division business to JJB in 1998, Sir Tom invested in property businesses in areas ranging from retail parks to hotels through West Coast Capital Holdings.
The venture suffered hefty losses on some of its investments after the property market went into reverse in 2007.
The latest accounts for West Coast Capital Holdings filed at Companies House show the company provided £61.7m against the value of its investments in the year ended 30 March. The company had accumulated losses of £93m at that date.
The West Coast Trading business provided another £13m against the valuation of its portfolio in the 14 months ended 31 March, taking the total value of such provisions to more than £100m.
While the retail operation made big gains on its investment in the successful Office footwear chain, it has suffered losses on others over time, such as the USC clothing chain.
The company cut pre-tax losses to £8m in the 14 months to March, from £16.4m in the preceding period. It booked a further £11.5m gain on the sale of its stake in Office, which was agreed in December 2010.
With accumulated losses of £215m at 31 March the company had negative net assets of £58.5m at 31 March.
West Coast Capital Holdings had net assets of £107.7m at 30 March. The company's investments were valued at £144.7m in its accounts.
During the periods concerned Sir Tom converted £163.8m loans owed by West Coast Capital Holdings and £ 150.9m owed by West Coast Capital Trading into shares.
A spokesman for West Coast Capital said: "Recapitalising the debt significantly strengthens these balance sheets and puts us in a debt free position as we seek to capitalise on market opportunities.
"We continue to see those opportunities predominantly in the property sector where we have a sizeable and growing portfolio."
He added: "With a policy of writing down assets and never writing values back up we are very content with the residual values within this portfolio."