To add to what macuser_22 said, the change in value between the time of the in-kind distribution and the rollover contribution of those same shares is irrelevant, even though the receiving custodian must report on Form 5498 the value of the rollover contribution based on the value at the time of the rollover contribution. The dollar amount of the rollover is based on the value of the shares at the time of the distribution, not the value when the rollover contribution is made.
Personally, I would anticipate that the IRS would question the amount actually rolled over and include a written statement with my filed tax return explaining that the rollover was the rollover of the same shares distributed as an in-kind distribution. The IRS has recently been increasing the scrutiny of rollovers and has automated systems to compare tax returns with Forms 1099-R and 5498.
