Liquidated damages are enforcable and should allways be considered when encoutering any delay. The concept of liquidated damages is that the owner will experience costs due to a delay due soley to the contactor or events reasonably anticipated by the contractor. The damages do not have to match the costs incurred by the owner, but must be a reasonable approximation with a rational derivation. Many contracts are not.You say this is an interim project milestone - does he owner realy absorb any cost due to a delay at this point if the schedule for the project were recovered? Second any delays for which the owner is responsible (late plans, design changes, access rights) are excusable, if not compensible. However, if you have signed change orders for work that has not added additional time to the contract, it will be very hard to claim delay. Also contracts generally have notice provisiuons for changes. Although these are enforcable, they often ae not as enforcible as owners would like to believe. As long as the owwner or his rep has reasonable knowledge of the delay, you can work from there. Hopefully you have documented these delays with the owner. It is possible to have excessive bad weather as a Force Majure(and therefore excusable). Documentng excessively bad weather does take work and really, unless blatent, can be a matter of opinion.
If you are being assessed liqudated damages, you should have a GOOD construction attorney involved now.As in today.
Good Luck